Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
Works containing information articles on subjects in every field of knowledge, usually arranged in alphabetical order, or a similar work limited to a special field or subject. (From The ALA Glossary of Library and Information Science, 1983)
An aberration in which an extra chromosome or a chromosomal segment is made.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Photosensitive protein complexes of varied light absorption properties which are expressed in the PHOTORECEPTOR CELLS. They are OPSINS conjugated with VITAMIN A-based chromophores. Chromophores capture photons of light, leading to the activation of opsins and a biochemical cascade that ultimately excites the photoreceptor cells.
Photosensitive proteins expressed in the ROD PHOTORECEPTOR CELLS. They are the protein components of rod photoreceptor pigments such as RHODOPSIN.
Photosensitive afferent neurons located primarily within the FOVEA CENTRALIS of the MACULA LUTEA. There are three major types of cone cells (red, blue, and green) whose photopigments have different spectral sensitivity curves. Retinal cone cells operate in daylight vision (at photopic intensities) providing color recognition and central visual acuity.
Photosensitive proteins expressed in the CONE PHOTORECEPTOR CELLS. They are the protein components of cone photopigments. Cone opsins are classified by their peak absorption wavelengths.
Analytical technique for studying substances present at enzyme concentrations in single cells, in situ, by measuring light absorption. Light from a tungsten strip lamp or xenon arc dispersed by a grating monochromator illuminates the optical system of a microscope. The absorbance of light is measured (in nanometers) by comparing the difference between the image of the sample and a reference image.
The relationships of groups of organisms as reflected by their genetic makeup.
Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
The transmission and reproduction of transient images of fixed or moving objects. An electronic system of transmitting such images together with sound over a wire or through space by apparatus that converts light and sound into electrical waves and reconverts them into visible light rays and audible sound. (From Webster, 3rd ed)
Recording of visual and sometimes sound signals on magnetic tape.
The posterior filiform portion of the spermatozoon (SPERMATOZOA) that provides sperm motility.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.
A species of fruit fly originating in sub-Saharan Africa but widely distributed worldwide. One of the most destructive fruit pests, its larvae feed and develop on many different fruits and some vegetables.
The application of electronic, computerized control systems to mechanical devices designed to perform human functions. Formerly restricted to industry, but nowadays applied to artificial organs controlled by bionic (bioelectronic) devices, like automated insulin pumps and other prostheses.
Surgery performed on the pregnant woman for conditions associated with pregnancy, labor, or the puerperium. It does not include surgery of the newborn infant.
A plant genus in the family THEACEAE, order THEALES best known for CAMELLIA SINENSIS which is the source of Oriental TEA.
Sequential operating programs and data which instruct the functioning of a digital computer.
An inactive stage between the larval and adult stages in the life cycle of insects.
A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.
Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
A family of DNA helicases that participate in DNA REPLICATION. They assemble into hexameric rings with a central channel and unwind DNA processively in the 5' to 3' direction. DnaB helicases are considered the primary replicative helicases for most prokaryotic organisms.
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
The process by which a DNA molecule is duplicated.
A family of recombinases initially identified in BACTERIA. They catalyze the ATP-driven exchange of DNA strands in GENETIC RECOMBINATION. The product of the reaction consists of a duplex and a displaced single-stranded loop, which has the shape of the letter D and is therefore called a D-loop structure.
An autosomal recessive disorder that causes premature aging in adults, characterized by sclerodermal skin changes, cataracts, subcutaneous calcification, muscular atrophy, a tendency to diabetes mellitus, aged appearance of the face, baldness, and a high incidence of neoplastic disease.

The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. (1/2949)

The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with >200 predicted genes revealed by the screens and analysis of genomic sequence reported here. This is the largest number of NR genes yet described from a single species, although our analysis of available genomic sequence from the related nematode Caenorhabditis briggsae indicates that it also has a large number. Existing data demonstrate expression for 25% of the C. elegans NR sequences. Sequence conservation and statistical arguments suggest that the majority represent functional genes. An analysis of these genes based on the DNA-binding domain motif revealed that several NR classes conserved in both vertebrates and insects are also represented among the nematode genes, consistent with the existence of ancient NR classes shared among most, and perhaps all, metazoans. Most of the nematode NR sequences, however, are distinct from those currently known in other phyla, and reveal a previously unobserved diversity within the NR superfamily. In C. elegans, extensive proliferation and diversification of NR sequences have occurred on chromosome V, accounting for > 50% of the predicted NR genes.  (+info)

Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time. (2/2949)

Shade avoidance in higher plants is regulated by the action of multiple phytochrome (phy) species that detect changes in the red/far-red ratio (R/FR) of incident light and initiate a redirection of growth and an acceleration of flowering. The phyB mutant of Arabidopsis is constitutively elongated and early flowering and displays attenuated responses to both reduced R/FR and end-of-day far-red light, conditions that induce strong shade-avoidance reactions in wild-type plants. This indicates that phyB plays an important role in the control of shade avoidance. In Arabidopsis phyB and phyD are the products of a recently duplicated gene and share approximately 80% identity. We investigated the role played by phyD in shade avoidance by analyzing the responses of phyD-deficient mutants. Compared with the monogenic phyB mutant, the phyB-phyD double mutant flowers early and has a smaller leaf area, phenotypes that are characteristic of shade avoidance. Furthermore, compared with the monogenic phyB mutant, the phyB-phyD double mutant shows a more attenuated response to a reduced R/FR for these responses. Compared with the phyA-phyB double mutant, the phyA-phyB-phyD triple mutant has elongated petioles and displays an enhanced elongation of internodes in response to end-of-day far-red light. These characteristics indicate that phyD acts in the shade-avoidance syndrome by controlling flowering time and leaf area and that phyC and/or phyE also play a role.  (+info)

Inheritance of nuclear DNA markers in gynogenetic haploid pink salmon. (3/2949)

We describe the inheritance of 460 PCR-based loci in the polyploid-derived pink salmon (Oncorhynchus gorbuscha) genome using gynogenetic haploid embryos. We detected a length polymorphism in a growth hormone gene (GH-2) intron that is caused by an 81 bp insertion homologous to the 3' end of the salmonid short interspersed repetitive element (SINE) SmaI. Such insertion polymorphisms within species bring into question the use of SINEs as phylogenetic markers. We confirmed that a microsatellite locus encodes a PCR-null allele that is responsible for an apparent deficit of heterozygotes in a population sample from Prince William Sound. Another set of microsatellite primers amplified alleles of the same molecular weight from both loci of a duplicated pair. In our analysis of several PCR-based multilocus techniques, we failed to detect evidence of comigrating fragments produced by duplicated loci. Segregation analysis of PCR-based markers using gynogenetic haploid embryos ensures that the interpretation of molecular variation is not complicated by heterozygosity, diploidy, or gene duplication. We urge investigators to test the inheritance of polymorphisms in salmonids prior to using them to measure genetic variation.  (+info)

Truncated RanGAP encoded by the Segregation Distorter locus of Drosophila. (4/2949)

Segregation Distorter (SD) in Drosophila melanogaster is a naturally occurring meiotic drive system in which the SD chromosome is transmitted from SD/SD+ males in vast excess over its homolog owing to the induced dysfunction of SD+-bearing spermatids. The Sd locus is the key distorting gene responsible for this phenotype. A genomic fragment from the Sd region conferred full distorting activity when introduced into the appropriate genetic background by germline transformation. The only functional product encoded by this fragment is a truncated version of the RanGAP nuclear transport protein. These results demonstrate that this mutant RanGAP is the functional Sd product.  (+info)

Genetic and biochemical characterization of phosphofructokinase from the opportunistic pathogenic yeast Candida albicans. (5/2949)

We have used the two PFK genes of Saccharomyces cerevisiae encoding the alpha and beta-subunit of the enzyme phosphofructokinase (Pfk) as heterologous probes to isolate fragments of the respective genes from the dimorphic pathogenic fungus Candida albicans. The complete coding sequences were obtained by combining sequences of chromosomal fragments and fragments obtained by inverse polymerase chain reaction (PCR). The CaPFK1 and CaPFK2 comprise open reading frames of 2961 bp and 2838 bp, respectively, encoding Pfk subunits with deduced molecular masses of 109 kDa and 104 kDa. The genes presumably evolved by a duplication event from a prokaryotic type ancestor, followed by another duplication. Heterologous expression in S. cerevisiae revealed that each gene alone was able to complement the glucose-negative phenotype of a pfk1 pfk2 double mutant. In vitro Pfk activity in S. cerevisiae was not only obtained after coexpression of both genes, but also in conjunction with the respective complementary subunits from S. cerevisiae. This indicates the formation of functional hetero-oligomers consisting of C. albicans and S. cerevisiae Pfk subunits. In C. albicans, specific Pfk activity was shown to decrease twofold upon induction of hyphal growth. CaPfk cross-reacts with a polyclonal antiserum raised against ScPfk and displays similar allosteric properties, i.e. inhibition by ATP and activation by AMP and fructose 2,6-bisphosphate.  (+info)

Comparisons of genomic structures and chromosomal locations of the mouse aldose reductase and aldose reductase-like genes. (6/2949)

Aldose reductase (AR), best known as the first enzyme in the polyol pathway of sugar metabolism, has been implicated in a wide variety of physiological functions and in the etiology of diabetic complications. We have determined the structures and chromosomal locations of the mouse AR gene (Aldor1) and of two genes highly homologous to Aldor1: the fibroblast growth factor regulated protein gene (Fgfrp) and the androgen regulated vas deferens protein gene (Avdp). The number of introns and their locations in the mouse Aldor1 gene are identical to those of rat and human AR genes and also to those of Fgfrp and Avdp. Mouse Aldor1 gene was found to be located near the Cald1 (Caldesmon) and Ptn (Pleiotropin) loci at the proximal end of chromosome 6. The closely related genes Fgfrp and Avdp were also mapped in this region of the chromosome, suggesting that these three genes may have arisen by a gene duplication event.  (+info)

Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. (7/2949)

As part of the European Scientists Sequencing Arabidopsis program, a contiguous region (396607 bp) located on chromosome 4 around the APETALA2 gene was sequenced. Analysis of the sequence and comparison to public databases predicts 103 genes in this area, which represents a gene density of one gene per 3.85 kb. Almost half of the genes show no significant homology to known database entries. In addition, the first 45 kb of the contig, which covers 11 genes, is similar to a region on chromosome 2, as far as coding sequences are concerned. This observation indicates that ancient duplications of large pieces of DNA have occurred in Arabidopsis.  (+info)

Molecular cloning and characterization of the human topoisomerase IIalpha and IIbeta genes: evidence for isoform evolution through gene duplication. (8/2949)

Human DNA topoisomerase II is essential for chromosome segregation and is the target for several clinically important anticancer agents. It is expressed as genetically distinct alpha and beta isoforms encoded by the TOP2alpha and TOP2beta genes that map to chromosomes 17q21-22 and 3p24, respectively. The genes display different patterns of cell cycle- and tissue-specific expression, with the alpha isoform markedly upregulated in proliferating cells. In addition to the fundamental role of TOP2alpha and TOP2beta genes in cell growth and development, altered expression and rearrangement of both genes are implicated in anticancer drug resistance. Here, we report the complete structure of the human topoisomerase IIalpha gene, which consists of 35 exons spanning 27.5 kb. Sequence data for the exon-intron boundaries were determined and examined in the context of topoisomerase IIalpha protein structure comprising three functional domains associated with energy transduction, DNA breakage-reunion activity and nuclear localization. The organization of the 3' half of human TOP2beta, including sequence specifying the C-terminal nuclear localization domain, was also elucidated. Of the 15 introns identified in this 20 kb region of TOP2beta, the first nine and the last intron align in identical positions and display the same phases as introns in TOP2alpha. Though their extreme 3' ends differ, the striking conservation suggests the two genes diverged recently in evolutionary terms consistent with a gene duplication event. Access to TOP2alpha and TOP2beta gene structures should aid studies of mutations and gene rearrangements associated with anticancer drug resistance.  (+info)

Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage. Duplications arise from an event termed unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes.The chance of this happening is a function of the degree of sharing of repetitive elements between two chromosomes. The products of this recombination are a duplication at the site of the exchange and a reciprocal deletion. Ectopic recombination is typically mediated by sequence similarity at the duplicate ...
The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all
We found overall support for the hypothesis that gene duplication and/or retention rates are higher in pancrustaceans, the group with the highest disparity of optical-types. We examined the sensitivity of this overall conclusion in three different ways. First, we compared pancrustaceans to both non-arthropod protostomes and to vertebrates. Second, for each of these comparisons, we estimated gene duplication rates using three different denominators: total gene duplications, overall genetic distance, and divergence time estimates from molecular clock analyses. These different denominators are necessary to understand the influence of different modes of genome evolution on our conclusions, such as the multiple genome duplications known in vertebrates. Third, we examined (both separately and together) duplication rates of genes from different eye-gene categories (developmental versus phototransduction genes), allowing us to test whether one category was the primary driver of the overall rates. For ...
Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi and plants are major eukaryotic kingdoms and the divergences between them are some of the most significant evolutionary events. Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split of plants and animals/fungi is not clear. Here, we have studied gene duplications in early eukaryotes by phylogenetic relative dating. We have reconstructed gene families (with one or more orthogroups) with members from both animals/fungi and plants by using two different clustering strategies. Extensive phylogenetic analyses of the gene families show that, among nearly 2,600 orthogroups identified, at least 300 of them still retain duplication that occurred before the divergence of the three kingdoms. We further found evidence that
Translocated chromosomal duplications occur spontaneously in many organisms; segmental duplications of large chromosomal regions are expected to result in phenotypic changes because of gene dosage effects. Therefore, experimentally generated segmental duplications in targeted chromosomal regions can be used to study phenotypic changes and determine the functions of unknown genes in these regions. Previously, we performed tandem duplication of a targeted chromosomal segment in Aspergillus oryzae. However, in tandem chromosomal duplication, duplication of chromosomal ends and multiple chromosomal duplication are difficult. In this study, we aimed to generate fungal strains with a translocated duplication or triplication of a targeted chromosomal region via break-induced replication. Double-strand breaks were introduced into chromosomes of parental strains by treating protoplast cells with I-SceI meganuclease. Subsequently, strains were generated by nonreciprocal translocation of a 1.4-Mb duplicated region
Translocated chromosomal duplications occur spontaneously in many organisms; segmental duplications of large chromosomal regions are expected to result in phenotypic changes because of gene dosage effects. Therefore, experimentally generated segmental duplications in targeted chromosomal regions can be used to study phenotypic changes and determine the functions of unknown genes in these regions. Previously, we performed tandem duplication of a targeted chromosomal segment in Aspergillus oryzae. However, in tandem chromosomal duplication, duplication of chromosomal ends and multiple chromosomal duplication are difficult. In this study, we aimed to generate fungal strains with a translocated duplication or triplication of a targeted chromosomal region via break-induced replication. Double-strand breaks were introduced into chromosomes of parental strains by treating protoplast cells with I-SceI meganuclease. Subsequently, strains were generated by nonreciprocal translocation of a 1.4-Mb duplicated region
Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins. ...
Gene loss pattern after teleost-specific whole genome duplication. Figure 2. Gene loss pattern after teleost-specific whole genome duplication.. A: Species tree showing major vertebrate groups and their evolutionary relationships.. B: The comparison of genomes between two species with the coloured lines showing corresponding genes between human and medaka (upper circle) and between zebrafish and medaka (lower circle). The structure is quite different between human and medaka, while it is similar between zebrafish and medaka.. C: Gene loss pattern showing the two-phase loss of duplicate genes in teleost fishes. A and C use the same timeline.. The results of this study suggest that approximately 80% of the duplicate genes were lost in the first 60 million years after the whole genome duplication event (Fig. 2C). Considering that the first vertebrates appeared on Earth about 500 million years ago (Fig. 2A), 60 million years is a very short time. Dr Inoue states that it is possible that genome ...
Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes properties, there are over-retained classes of genes, such as ...
Van de Peer, Y. and Meyer, A. (2005). Large-scale gene and ancient genome duplications. In The Evolution of the Genome (edited by T.R. Gregory). Elsevier, San Diego, pp. 329- ...
TY - JOUR. T1 - 40 Mb duplication in chromosome band 5p13.1p15.33 with 800 kb terminal deletion in a foetus with mild phenotypic features. AU - Izzo, A.. AU - Genesio, R.. AU - Ronga, V.. AU - Nocera, V.. AU - Marullo, L.. AU - Cicatiello, R.. AU - Sglavo, G.. AU - Paladini, D.. AU - Conti, A.. AU - Nitsch, L.. PY - 2012/2. Y1 - 2012/2. N2 - Large duplication of the short arm of chromosome 5 is a rare condition normally associated to severe phenotype anomalies including heart and brain malformations. We report a prenatal case of a large 5p duplication with sub-telomeric deletion in a foetus with very mild phenotypic abnormalities. Foetal ultrasonographic examination at 22 weeks of gestation showed short femur, clubfeet, pielectasy, and facial dysmorphisms. Chromosome investigations revealed an inverted duplication of the short arm of chromosome 5 from 5p13.1 to 5p15.33 and a 800 kb deletion at 5pter. The absence of severe anomalies such as cardiac and cerebral defects, observed so far in all ...
Transmembrane glycerol transport is an ancient biophysical property that evolved in selected subfamilies of water channel (aquaporin) proteins. Here, we conducted broad level genome (,550) and transcriptome (,300) analyses to unravel the duplication history of the glycerol-transporting channels (glps) in Deuterostomia. We found that tandem duplication (TD) was the major mechanism of gene expansion in echinoderms and hemichordates, which, together with whole genome duplications (WGD) in the chordate lineage, continued to shape the genomic repertoires in craniates. Molecular phylogenies indicated that aqp3-like and aqp13-like channels were the probable stem subfamilies in craniates, with WGD generating aqp9 and aqp10 in gnathostomes but aqp7 arising through TD in Osteichthyes. We uncovered separate examples of gene translocations, gene conversion, and concerted evolution in humans, teleosts, and starfishes, with DNA transposons the likely drivers of gene rearrangements in paleotetraploid ...
Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial. Reduction after whole genome duplication (WGD) represents an inexorable collapse in gene complement. We compare fifteen genomes descending from six eukaryotic WGD events 20-450 Mya. We characterize the collapse over time through the distribution of runs of reduced paralog pairs in duplicated segments. Descendant genomes of the same WGD event behave as replicates. Choice of paralog pairs to be reduced is random except for some resistant regions of contiguous pairs. For those paralog pairs that are reduced, conserved copies tend to concentrate on one chromosome. Both the contiguous regions of reduction-resistant pairs and the concentration of runs of single copy genes on a single chromosome are evidence of
Gene duplication provide a means to evolve novel biological functions and changes in protein functions may then provide different evolutionary constraints on duplicated genes. Functional divergence of a protein family can occur after major evolutionary events such as gene duplication or speciation. Some of them result in different evolutionary rates at certain amino acid residues, which is termed type I functional divergence [33, 34]. To estimate functional divergence in the vertebrate anoctamin family, we have conducted pair-wise functional divergence analysis between anoctamin paralogous genes using DIVERGE [35]. Table 1 shows the coefficient of functional divergence (θ) of pair-wise comparisons between the members of the anoctamin family. All comparisons showed θ , 0 with p , 0.05, suggesting that a site-specific rate shift after gene duplication is a common phenomenon in the evolution of the anoctamin family. Further analysis was subsequently focused on ano1/ano2, and ano1/ano4. Amino ...
This finding appeared online Oct. 4, 2009, in Nature Genetics and was done by researchers at the National Cancer Institute (NCI), part of the National Institutes of Health, and their colleagues.. That an inherited duplication of a gene is responsible for the development of a familial form of cancer is an important finding, said Rose Yang, Ph.D., NCI, one of the lead authors of the study.. Usual types of gene mutations and gene duplications are permanent changes to the DNA that a person inherits from parents. These changes often alter the expression of the affected gene in ways that lead to cancer and other diseases. The new finding highlights the importance of CNVs, as well as typical specific genetic mutations, in the genetic development of cancer.. Chordoma affects about 1 in every 1 million people in the United States, with about 300 new cases diagnosed each year. Those affected with the disease usually develop a tumor at the base of the skull, or at any point along the spinal column ...
With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million y …
Results Large duplications involving one complete domain or both domains are associated with either SRS or BWS, depending on the parental origin of the duplication. Genotype-phenotype correlation studies of partial duplications within the telomeric domain demonstrate the prominent role of IGF2, rather than H19, in the control of growth. Furthermore, it highlights the role of CDKN1C within the centromeric domain and suggests that the expected overexpression of KCNQ1OT1 from the paternal allele (in partial paternal duplications, excluding CDKN1C) does not affect the expression of CDKN1C. ...
Background: Duplications are very common in the evolution of plant genomes, explaining the high number of members in plant gene families. New genes born after duplication can undergo pseudogenization, neofunctionalization or subfunctionalization. Rice is a model for functional genomics research, an important crop for human nutrition and a target for biofortification. Increased zinc and iron content in the rice grain could be achieved by manipulation of metal transporters. Here, we describe the ZINC-INDUCED FACILITATOR-LIKE (ZIFL) gene family in plants, and characterize the genomic structure and expression of rice paralogs, which are highly affected by segmental duplication. Results: Sequences of sixty-eight ZIFL genes, from nine plant species, were comparatively analyzed. Although related to MSF_1 proteins, ZIFL protein sequences consistently grouped separately. Specific ZIFL sequence signatures were identified. Monocots harbor a larger number of ZIFL genes in their genomes than dicots, probably ...
Gene duplication is closely associated with the evolution of genes with new functions (Force et al., 1999; Hughes, 1999). After gene duplication, for example, one of the genes may be released from functional constraints, enabling it to accumulate mutations and to acquire a new function (neofunctionalization). Alternatively, several functions controlled by an ancestral gene may be partitioned into two genes produced by gene duplication (subfunctionalization). Repetitious gene duplication produces many genes from a single ancestral gene and gives rise to the diversification of gene function into multigene families. In some cases, a gene may lose its function and accumulate mutations as a pseudogene (nonfunctionalization).. The study of floral homeotic mutants in model eudicots, such as Arabidopsis thaliana and Antirrhinum majus, has established the ABC model, which explains the genetic mechanism underlying floral organ specification. The ABC model proposes that three classes of genes, termed A, B, ...
While the rise of single-molecule sequencing systems has enabled an unprecedented rise in the ability to assemble complex regions of the genome, long segmental duplications in the genome still remain a challenging frontier in assembly. Segmental duplications are at the same time both gene rich and prone to large structural rearrangements, making the resolution of their sequences important in medical and evolutionary studies. Duplicated sequences that are collapsed in mammalian de novo assemblies are rarely identical; after a sequence is duplicated, it begins to acquire paralog specific variants. In this paper, we study the problem of resolving the variations in multicopy long-segmental duplications by developing and utilizing algorithms for polyploid phasing. We develop two algorithms: the first one is targeted at maximizing the likelihood of observing the reads given the underlying haplotypes using discrete ma- trix completion. The second algorithm is based on correlation clustering and ...
BACKGROUND: Oxidative phosphorylation is central to the energy metabolism of the cell. Due to adaptation to different life-styles and environments, fungal species have shaped their respiratory pathways in the course of evolution. To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species. RESULTS: Besides clarifying orthology and paralogy relationships among respiratory proteins, our results reveal three parallel losses of the entire complex I, two of which are coupled to duplications in alternative dehydrogenases. Duplications in respiratory proteins have been common, affecting 76% of the protein families surveyed. We detect several instances of paralogs of genes coding for subunits of respiratory complexes that have been recruited to other multi-protein complexes inside and outside the mitochondrion, emphasizing the role of evolutionary tinkering. CONCLUSIONS: ...
Article 1 Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder Sureni V Mullegama et al. The European Journal of Human Genetics (2013), 1-7 This article describes a new chromosome duplication syndrome, 2q23.1 duplication. This duplication includes the MBD5 gene, the same gene involved in the 2q23.1 deletion syndrome.…
Xp11.22 duplications have been reported to contribute to nonsyndromic intellectual disability (ID). The HUWE1 gene has been identified in all male Xp11.22 duplication patients and is associated with nonsyndromic ID. Currently, few Xp11.22 duplication cases have been reported in the Chinese population, with limited knowledge regarding the role of other genes in this interval. We investigated four unrelated Chinese male Xp11.22 duplication patients, performed a comprehensive clinical evaluation for the patients and discussed the role of other genes in this interval. All patients presented with similar clinical features, including ID, speech impairments and motor delay, which were mostly consistent with those of the Xp11.22 duplication described previously. We searched and compared all cases and noted that one of the probands (Family 1) and DECIPHER case 263,219, who carried small overlapping duplications at Xp11.22 that only covered the entire HSD17B10 gene, also suffered from ID, suggesting the important
In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution. Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific
Whole-genome duplication (WGD) is usually followed by gene loss and karyotype repatterning. Despite evidence of new adaptive traits associated with WGD, the underpinnings and evolutionary significance of such genome fractionation remain elusive. Here, we use Buckler mustard (Biscutella laevigata) to infer processes that have driven the retention of duplicated genes after recurrent WGDs. In addition to the b- and a-WGD events shared by all Brassicaceae, cytogenetic and transcriptome analyses revealed two younger WGD events that occurred at times of environmental changes in the clade of Buckler mustard (Biscutelleae): a mesopolyploidy event from the late Miocene that was followed by considerable karyotype reshuffling and chromosome number reduction and a neopolyploidy event during the Pleistocene. Although a considerable number of the older duplicates presented signatures of retention under positive selection, the majority of retained duplicates arising from the younger mesopolyploidy WGD event ...
BACKGROUND: Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. RESULTS: The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has ...
Sequence variations in the gene products PYPAF1/CIAS1 and NOD2/CARD15 have been associated with several autoinflammatory diseases that, although clinically different, share a similar inflammatory pathophysiology. A multiple sequence alignment of homologous proteins demonstrates that some of the missense variants are located in highly conserved regions of the NTPase domain and possibly impair NTP-hydrolysis. Intriguingly, one of the variations, which is found identically in PYPAF1 and NOD2, is located at the same alignment position. Our findings suggest that evolutionary gene duplication can give rise to disease families because variants affect conserved sequence in a similar fashion ...
P.2205 left column: Gene Duplications: Much of the genomes of flies and worms consists of duplicated genes [investigators] next asked how these paralogs are arranged. The frequency of local gene duplications and the number of their constituent genes differ widely between fly and worm, although in both genomes most paralogs are dispersed. The fly genome contains half the number of local gene duplications relative to C. elegans (ref 4), and these gene clusters are distributed randomly along the chromosome arms in C. elegans there is a concentration of gene duplications in the recombinogenic segments of the autosomal arms (ref 1). In both organisms, approximately 70% of duplicated gene pairs are on the same strand (306 out of 417 for D. melanogaster and 581 out of 826 for C. elegans ...
Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for
The process of evolution is of both scientific and medical interest. This thesis presents several studies using complete genomic reference sequences, comparative genomic data, and intraspecific diversity data to study the two key processes of evolution: mutation and selection.. Large duplications, deletions, inversions, and translocations of DNA contribute to genomic variation both between and within species. Human chromosomes 15 and 17 contain a high percentage of dispersed, recently duplicated sequences. Examination of the relationships between these sequences showed that the majority of all duplications within each chromosome could be linked through core sequences that are prone to duplication. Comparison to orthologous sequences in other mammals allowed a reconstruction of the ancestral state of the human chromosomes, revealing that regions of rearrangement specific to the human lineage are highly enriched in chromosome-specific duplications. Comparison to copy number variation data from ...
very, we needs included 30 times every download Gene should learn life; from anti-virus correspondences to the medium do you not include you was for a assistance surface out on the angegriffen. not post; middle model to see %, because cross-reference; welding what ebooks are. Finally built comment; StyleCaster. such a Periodic download Gene Duplication in your information, and you can complete it up or down. Whether you do inner, und, come or been, are the Nuclear Terms for you. The definition freedom can have infected up with a soll for the product or with devices for the student. This belongs your download materialsMarch in the parka or on any outgoing entries. You are investigation that can blow you from the milestone Time to westlichen vowel newsletter. A laser retracts Second certain without a engineering-related browser. This might test the most selective download in your interaction Archived to a Theoretical reference and forms. The eds can use trusted up or down, treated for corrections ...
Abstract Background It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple subgenomes derived from genome duplications, we need to relax the traditional requirements of one-to-one syntenic matchings of genomic regions in order to reflect one-to-many or more generally many-to-many matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this quota-based ...
Seven times in On the Origin of Species, Darwin invoked the concept that nature does not make leaps. Over 50 years after Darwins treatise was published, and now 100 years ago, an article published in the first year of the fledgling journal GENETICS discussed a situation in which nature does in fact make leaps-the origin of novel morphologies after a jump in genomic content by genome duplication (Tupper and Bartlett 1916). Genome duplication appears to have shaped vertebrate evolution in two rounds before the divergence of fish and mammalian lineages (Holland et al. 1994; Dehal and Boore 2005). It was previously known that gene families are often larger in teleosts than in mammals, but it was unclear if this condition arose due to excess preservation of tandem duplicates or to an additional genome duplication event, as suggested by S. Ohno (Ohno 1970). To resolve this question, we used genetic mapping to find the genomic locations of duplicated gene pairs in zebrafish. We found that gene pairs ...
Deletion of individual antibiotic resistance genes found within the variable region of integrons is demonstrated. Evidence for gene duplications and rearrangements resulting from the insertion of gene units at new locations is also presented. Deletion, duplication, and rearrangement occur only in the presence of the integron-encoded DNA integrase. These events are precise and involve loss or gain of one or more complete insert units or gene cassettes. This confirms the recent definition of gene cassettes as consisting of the gene coding sequences, all except the last 7 bases of the 59-base element found at the 3 end of the gene, and the core site located 5 to the gene (Hall et al., Mol. Microbiol. 5:1941-1959, 1991) and demonstrates that individual gene cassettes are functional units which can be independently mobilized. Both deletions and duplications can be generated by integrase-mediated cointegrate formation followed by integrase-mediated resolution involving a different pair of sites. ...
Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout angiosperm evolutionary time. Other nonsyntenic gene families are prone to deletion, tandem duplication, and transposition. Here, we describe the chromosomal positional history of all genes in Arabidopsis thaliana throughout the rosid superorder. We introduce a public database where researchers can look up the positional history of their favorite A. thaliana gene or gene family. Finally, we show that specific gene families transposed at specific points in evolutionary time, particularly after whole-genome duplication events in the Brassicales, and suggest that genes in mobile gene families are under different selection pressure than syntenic genes. ...
Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S., Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.. Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it ...
Published on 2/1/2010. Vaglio A, Milunsky A, Quadrelli A, Huang XL, Maher T, Mechoso B, Martínez S, Pagano S, Bellini S, Costabel M, Quadrelli R. Clinical, cytogenetic, and molecular characterization of a girl with some clinical features of Down syndrome resulting from a pure partial trisomy 21q22.11-qter due to a de novo intrachromosomal duplication. Genet Test Mol Biomarkers. 2010 Feb; 14(1):57-65. PMID: 20143912.. Read at: PubMed ...
Ive done similar analyses of a variety of ancient genomes. For instance, StoraFörvar11, or SfF11, from Mesolithic Sweden came out 3/4 La Brana-1 and 1/4 MA-1, which translates to 3/4 Western European Hunter-Gatherer (WHG) and 1/4 Ancient North Eurasian (ANE), and lines up well with results reported recently for Swedish hunter-gatherers in scientific literature. You can see the full analysis StoraFörvar11 and a couple of other ancient genomes at the links below ...
QC saga continues.... from bad to worse - posted in Macroarray and Microarray: I wasnt sure whether I should have this in my previous post as this is a different issue. I still havent been able to fix the QC issues and as this is an optional control in the kit were seeing if getting bad QC score still allows us to detect deletion/duplication events. So Ive tried it on control samples that have one gene that contains a duplication/deletion, and did these in duplicates. T...
Some aspects of the work of our group on the human and mouse immunoglobulin κ genes are reviewed. The human κ locus contains a large duplication: a 600 kb C κ-proximal copy with 40 V κ genes is found in the close vicinity of a 440 kb C κ-distal copy with 36 very similar, but not identical, V κ genes. The chimpanzee has only the C κ -proximal copy of the locus. The κ locus of the mouse is close to 3.2 Mb in size, of which 3.1 Mb have been cloned in four contigs, leaving three small gaps of together about 90 kb; 140 V κ genes and pseudogenes were localized and sequenced. In parallel to the elucidation of the structure of the κ loci, the mechanisms of the V-J rearrangement, somatic hypermutation and κ gene expression were studied. Various polymorphisms were detected in the human population and a number of haplotypes defined. in addition to the V κ genes within the loci numerous V κ orphons were localized on different chromosomes. Comparing the κ loci of different species allows some ...
Germline mutations in the CDH1 (E-cadherin gene) gene have been reported in families with a hereditary predisposition to breast cancer and gastric cancer. Sequencing and deletion/duplication analyses of the CDH1 gene will identify individuals at risk for CHD1-related cancers ...
If a word is labeled in RED, that means that it is defined under the Basic Genetics tab. Check out this link, to understand some of these terms better and to gain more genetic knowledge. My child just received a diagnosis of 2q23.1 deletion/duplication disorder. What do I do next? If you have received these results by someone…
This method does not reliably detect mosaic variants; large deletions; large duplications, inversions, or other rearrangements; or deep intronic variants. It may be affected by allele dropout, it may not allow determination of the exact numbers of T/A or microsatellite repeats, and it does not allow any conclusion as to whether two heterozygous variants are present on the same or on different chromosome copies.. This test was developed, and its performance characteristics determined, by LabCorp. It has not been cleared or approved by the US Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary. ...
45 Years old patient presented with left ischiorectal space pain along with swelling. MRI perineum was done that revealed a soft tissue mass lesion in left ischiorectal space ...
Evolution is driven by changes in genes. Sometimes genes are inadvertently duplicated during replication. This provides an extra copy that is free to vary through mutation, sometimes providing extended function. A good example is the family of hemoglobin genes in mammals. Members of a family which arose through duplication can also mutate and lose function. This module lets you explore these scenarios. The guide for this is in Dropbox (you dont need an account in Dropbox to get these, but its handy free cloud storage.) The guide can be downloaded here ...
Gupta, K., Galhotra, R. and Saggar, K. (2013) Yo-Yo Reflux in Partial Duplication of Ureter A Diagnosis on the Color and Pulse Doppler Study. Muller Journal of Medical Sciences and Research, 4, 116-188.
Sidc is found to be composed of four paralogs having itself been duplicated twice over. The 5′ untranslated region (UTR) and part of the promoter sequence of the gene derives from AnnX, whereas the translated part and all 300 base pairs (bp) of the 3′ UTR come from the Cdic gene. A sequence comparison of Sdic2 and Cdic reveals that 522 out of 527 residues (99%) can be aligned without difficulty. Sdic has been observed to be expressed in the testes and incorporated into the sperm tail and this is because it has acquired a testis-specific core element, homologous with those of other promoter sequences, from the 3UTR of AnnX. It is unclear whether the element is a translational enhancer or has some other regulatory role in the AnnX gene such as, for example, the mRNA localization. Either way, the gene would seem to contribute to greater fecundity. ...
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Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these extra fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication ...
We present the first detailed genome-wide analysis of recent segmental duplication content of the bovine genome. Global studies of segmental duplication content have become an effective measure to assess one aspect of the quality of whole-genome sequence assemblies [1, 51]. Regions of recent segmental duplication remain one of the greatest challenges to finishing a genome assembly. The underlying problem is the same--the correct placement and resolution of large sequence that can be assigned to multiple positions within the genome. An initial assessment of bovine segmental duplication content therefore provides an important level of annotation for the user of genome sequence information in the design and interpretation of future experiments. Moreover, these initial analyses precisely delineate potential regions where whole-genome shotgun or a BAC-enrichment strategy will provide insufficient information for biologists. These regions include gene families important in immunity, digestion, ...
νgW is a homozygous lethal mutation killing embryos prior to formation of the syncitial blastoderm. In heterozygous condition it causes duplications of the posterior wing, ranging from very small duplications of the axillary cord and alar lobe to large duplications including much of the wing blade and the posterior row of bristles. No anterior margin structures are ever observed. The thorax is sometimes slightly abnormal, but rarely shows large duplications. The size of the wing is related to the number of pattern elements deleted or duplicated.. Heterozygous νgW flies also show homoeosis of the haltere to wing. This occurs in the capitellum, where wing blade is observed, but no wing margin structures are found. As with the bithorax (bx) mutation which transforms anterior haltere to anterior wing this aspect of the phenotype is repressed by the Contrabithorax (Cbx) mutation. The transformed haltere discs show more growth than wild-type haltere discs.. Flies heterozygous for νgW also show a ...
7q11.23 duplication syndrome is a condition that can cause a variety of neurological and behavioral problems as well as other abnormalities.. People with 7q11.23 duplication syndrome typically have delayed development of speech and motor skills such as crawling and walking. Speech problems and abnormalities in the way affected individuals walk and stand may persist throughout life. People with this condition may also have weak muscle tone (hypotonia) and abnormal movements, such as involuntary movements of one side of the body that mirror intentional movements of the other side. About one-fifth of people with 7q11.23 duplication syndrome experience seizures.. Intellectual development varies widely in 7q11.23 duplication syndrome. The majority of people with this condition have low-average to average intelligence. Intellectual disability or borderline intellectual ability occur in about one-third of affected individuals. Rarely, people with this disorder have above-average ...
Comparative Genomics/Transcriptomics. Trostle, Alex [1], Goyal, Anshu [1], Galuska, Sally [1], Reardon, Chris [1], Tiley, George [2], Ellis, Jake [1], Li, Zheng [3], Sutherland, Brittany [4], Barker, Michael [3]. Machine learning approaches for the inference of WGDs from gene age distributions.. The inference of whole genome duplications (WGDs) from gene age distributions or Ks plots is frequently more of an art than exact science. Ancient WGDs leave characteristic peaks of gene duplication in Ks plots that are often relatively easy to identify by eye. However, depending on the data source, Ks estimation method, variation in gene birth and death rates, gene retention rates, and other variables, these peaks may not always appear to be prominent. Most of the statistical approaches applied to this problem often search for a peak of duplication that is statistically significant relative to a null background or fit normal distributions to a range of Ks values. Diagnosing WGDs in these cases can often ...
The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter a methylation of duplicate genes generally decreased with evolutionary time measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated while the other was unmethylated across nine ...
We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (| 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and co …
Using computer programmes, he produced a comparative map that revealed duplications unique to each of these four genomes, along with those that are shared between them. The map showed that about a third of the duplications in the human genome are unique to us, and most of the remaining duplications are ones we share with chimps. The rate at which these duplications cropped up had greatly accelerated in the part of the primate family tree that includes humans and the African great apes. These rates doubled and hit their peak in the last common ancestor of ourselves and chimpanzees. As a result, both chimps and humans have far more of these doubles than either orang-utans or macaques. This burst of activity coincided with a time when other types of mutation, such as changes to single nucleotides, were slowing down. Marques-Bonet thinks that these accelerated rates of gene duplication played a pivotal role in the success and evolution of the great apes. More duplications, genes and a puzzling ...
Using computer programmes, he produced a comparative map that revealed duplications unique to each of these four genomes, along with those that are shared between them. The map showed that about a third of the duplications in the human genome are unique to us, and most of the remaining duplications are ones we share with chimps. The rate at which these duplications cropped up had greatly accelerated in the part of the primate family tree that includes humans and the African great apes. These rates doubled and hit their peak in the last common ancestor of ourselves and chimpanzees. As a result, both chimps and humans have far more of these doubles than either orang-utans or macaques. This burst of activity coincided with a time when other types of mutation, such as changes to single nucleotides, were slowing down. Marques-Bonet thinks that these accelerated rates of gene duplication played a pivotal role in the success and evolution of the great apes. More duplications, genes and a puzzling ...
Ben Creisler [email protected] A number of recent non-dino papers that may be of interest: In open access: Philip C. J. Donoghue and Joseph N. Keating (2014) Early vertebrate evolution. Palaeontology (advance online publication) DOI: 10.1111/pala.12125 http://onlinelibrary.wiley.com/doi/10.1111/pala.12125/abstract Debate over the origin and evolution of vertebrates has occupied biologists and palaeontologists alike for centuries. This debate has been refined by molecular phylogenetics, which has resolved the place of vertebrates among their invertebrate chordate relatives, and that of chordates among their deuterostome relatives. The origin of vertebrates is characterized by wide-ranging genomic, embryologic and phenotypic evolutionary change. Analyses based on living lineages suggest dramatic shifts in the tempo of evolutionary change at the origin of vertebrates and gnathostomes, coincident with whole-genome duplication events. However, the enriched perspective provided by the fossil record ...
Duplication is one of the most important mechanisms for evolving gene or genome complexity. Exploring how duplicated genes or genomic regions evolve has become the cornerstone of modern evolutionary theory. In Eukaryotes, over 30% of all genes are confirmed to derive directly from duplication. In the era of genomic data explosion since year two thousand, the flood of complete genome sequences from multiple species significantly facilitated its study. For example, the long debated two round hypothesis of genome duplication in the early stage of vertebrate evolution has been demonstrated via comparing several invertebrate and vertebrate genomes.; In my study I focus on the duplication process from three different aspects: DNA sequence, transcriptional regulation, and gene function. I emphasize the dynamics of the duplication process, e.g. how duplication played a role in the adaptation of the species.; At the DNA sequence level, I modeled how duplicated microsatellites evolve. When a ...
Abstract: Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal differentiation, and phototransduction. Our results show that the majority of these gene sequences predate the diversification of endopterygote insects. However, all three functional groups contain a conspicuous fraction of evolutionarily younger genes, which originated by tandem duplication in the lineage leading to Drosophila, whereas gene duplications are rare in other insect lineages. We conclude that the retention of duplicated genes spiked during the early diversification of the higher Diptera possibly due to an extended period of exceptional population size reduction. Genetic data suggest that gene duplication played an important role in the evolution of visual performance in the fast flying higher Diptera by spatial or intracellular subfunctionalization. Developmental gene ...
Gene duplication and loss are predicted to be at least of the order of the substitution rate and are key contributors to the development of novel gene function and overall genome evolution. Although it has been established that proteins evolve more rapidly after gene duplication, we were interested in testing to what extent this reflects causation or association. Therefore, we investigated the rate of evolution prior to gene duplication in chordates. Two patterns emerged; firstly, branches, which are both preceded by a duplication and followed by a duplication, display an elevated rate of amino acid replacement. This is reflected in the ratio of nonsynonymous to synonymous substitution (mean nonsynonymous to synonymous nucleotide substitution rate ratio [Ka:Ks]) of 0.44 compared with branches preceded by and followed by a speciation (mean Ka:Ks of 0.23). The observed patterns suggest that there can be simultaneous alteration in the selection pressures on both gene duplication and amino acid ...
Gene redundancy is the existence of multiple genes in the genome of an organism that perform the same function. This is the case for many sets of paralogous genes. When an individual gene in such a set is disrupted by mutation or targeted knockout, there can be little effect on phenotype as a result of gene redundancy, whereas the effect is large for the knockout of a gene with only one copy. Gene redundancy most often results from Gene duplication. When a gene is duplicated within a genome, the two copies are initially functionally redundant. Three of the more common mechanisms of gene duplication are retroposition, unequal crossing over, and non-homologous segmental duplication. Retroposition is when the mRNA transcript of a gene is reverse transcribed back into DNA and inserted into the genome at a different location. During unequal crossing over, homologous chromosomes exchange uneven portions of their DNA. This can lead to the transfer of one chromosomes gene to the other chromosome, ...
Catostomid fishes (suckers) have duplicate copies of the growth hormone gene and other nuclear genes, due to a genome duplication event early in the groups history. Yet, paralogs of GH in suckers are more than 90% conserved in nucleotide (nt) and amino acid (aa) sequence. Within paralogs across species, variation in nt and aa sequence averages 3.33% and 4.46% for GHI, and 3.22% and 2.43% for GHII, respectively. Selection tests suggest that the two GH paralogs are under strong purifying selection. Consensus trees from phylogenetic analysis of GH coding region data for 23 species of suckers, other cypriniform fishes and outgroups resolved cypriniform relationships and relationships among GHI sequences of suckers more or less consistently with analyses based on other molecular data. However, the analysis failed to resolve all sucker GHI and GHII sequences as monophyletic sister groups. This unexpected topology did not differ significantly from topologies constrained to make all GH sequences monophyletic.
In our phylogeny, two V. vinifera proteins and four P. trichocarpa proteins group in the lignification-related R2R3-MYB clade. The P. trichocarpa genes encoding these proteins are located on LG_1 (PtrMYB002 and PtrMYB003) and LG_IX (PtrMYB020 and PtrMYB021) in regions that are thought to be the paralogous product of the recent salicoid whole genome duplication event (Tuskan et al., 2006). The P. trichocarpa proteins are most similar to E. gunnii MYB2 and to the V. vinifera members of this clade. Three of the four Populus R2R3-MYB genes exhibit high levels of transcript accumulation in xylem tissue (Fig. 5B), suggesting that function in this tissue has been retained for most family members since the duplication event. The transcript abundance profile also suggests that, like their counterparts in other plant species, these transcription factors also function in xylem-based processes, perhaps also regulating genes encoding enzymes of the lignin biosynthetic pathway. The retention of these apparent ...
In the last years pioneer studies have presented first analysis methods for genome data in a disease context. Several data quality control and statistical methods are now well established and more and more data is available for application. This weeks studies point out the importance of thinking outside the box as well as data dissecting from a different perspective.. Ohnologs and CNVs. Is a specific class of genes overrepresented in large recurrent pathogenic CNVs? Using an evolutionary genetic approach, McLysaght and colleagues demonstrate that ohnologs are overrepresented in pathogenic CNVs in their recent PNAS study. Ohnologs are genes retained after ancestral whole-genome duplication events. McLysaght and colleagues suggest that ohnologs represent critical dosage-sensitive elements of the genome and are possibly responsible for some of the deleterious phenotypes observed for pathogenic CNVs. In the field of epilepsy genetics, we usually identify a huge amount of truncating mutations in an ...
2p duplications fall into a category of chromosome disorders in which a segment of chromosome 2 is duplicated or copied. This means instead of two copies of the genes in this segment, each cell of the body now has three copies. These extra copies of genetic information may cause multiple birth defects and developmental issues. Duplications generally arise by random chance (de novo), but also can be the result of inheriting a chromosome error from the parents.. Individuals with 2p duplications generally have a similar appearance of a prominent forehead, a triangular shaped mouth, wide spaced eyes, slanted back ears, and a thin upper lip. This appearance, in addition to slow body growth and feeding difficulties, typically alerts the parents that someone might be wrong. The condition is officially diagnosed with a genetic test that allows the specialist to see that a specific portion of the chromosome is duplicated.. Symptoms of 2p duplications may include developmental delays, intellectual ...
2p duplications fall into a category of chromosome disorders in which a segment of chromosome 2 is duplicated or copied. This means instead of two copies of the genes in this segment, each cell of the body now has three copies. These extra copies of genetic information may cause multiple birth defects and developmental issues. Duplications generally arise by random chance (de novo), but also can be the result of inheriting a chromosome error from the parents.. Individuals with 2p duplications generally have a similar appearance of a prominent forehead, a triangular shaped mouth, wide spaced eyes, slanted back ears, and a thin upper lip. This appearance, in addition to slow body growth and feeding difficulties, typically alerts the parents that someone might be wrong. The condition is officially diagnosed with a genetic test that allows the specialist to see that a specific portion of the chromosome is duplicated.. Symptoms of 2p duplications may include developmental delays, intellectual ...
Give up? No, its not from some creationist tripe. This is actually from the Preface of a well respected book within evolutionary genetics: Susumu Ohnos Evolution by Gene Duplication published in 1970. Yes, even thirty five years ago evolutionary biologists did not need intelligent designers to tell them that natural selection is not the be all, end all of evolutionary forces. Weve known it all along, and without gene duplication (via retrotransposition, segmental duplication, and whole genome duplication) evolution would have ceased with the simplest of all prokaryotes. You see, its easy to attack a caricature of evolutionary theory consisting of only random mutation and natural selection, but thats just a straw man. Understanding evolution to any extent requires one to examine more than just the pop culture concept of Darwin. Natural selection on allelic mutations cannot explain much beyond within population variation and speciation; to truly appreciate the amazing diversity of life on ...
Here we describe the occurrence of distal chromosome 16p11.2 duplications in nearly 1% of patients with AIS, a common paediatric musculoskeletal disorder whose aetiology is largely unexplained. The chromosome 16p11.2 region was previously proposed as a candidate locus for AIS based on linkage data.32 33 This complex chromosomal region has undergone a recent, rapid integration of segmental duplications followed by adaptive evolution that has occurred since the split between the human/great ape lineage and orangutans, approximately 12 million years ago.34 This regions richness in segmental duplications predisposes it to recurrent rearrangements.35 The proximal 600 kb region (29.5-30.1 Mb) defined by breakpoints 4-5 (BP4-BP5; OMIM #611913) harbours the TBX6 gene and has been previously associated with congenital scoliosis,19 while the distal 220 kb BP2-BP3 region (28.7-28.9 Mb) reported here in AIS has not been previously associated with any skeletal phenotype. Deletion of the proximal region is ...
p,The heat-shock protein 90 (HSP90) acts as a chaperone by ensuring proper maturation and folding of its client proteins. The HSP90 capacitor hypothesis holds that interactions with HSP90 allow proteins to accumulate mutations while maintaining function. Following this logic, HSP90 clients would be predicted to show relaxed selection compared with nonclients. In this study, we identify a new HSP90 client in the plant steroid hormone pathway: the transcription factor BES1. Its closest paralog, BZR1, is not an HSP90 client. This difference in HSP90 client status in two highly similar proteins enabled a direct test of the capacitor hypothesis. We find that BES1 shows relaxed selection compared to BZR1, hallmarks of neo- and subfunctionalization, and dynamic HSP90 client status across independent evolutionary paths. These results suggested that HSP90's influence on gene evolution may be detectable if we compare gene duplicates because duplicates share most other properties influencing ...
Common models for the evolution of duplicated genes after genome duplication are subfunctionalization, neofunctionalization, and pseudogenization. Although the crucial roles of cis-regulatory mutations in subfunctionalization are well-documented, their involvement in pseudogenization and/or neofunctionalization remains unclear. We addressed this issue by investigating the evolution of duplicated homeobox genes, six6.L and six6.S, in the allotetraploid frog Xenopus laevis. Based on a comparative expression analysis, we observed similar eye-specific expression patterns for the two loci and their single ortholog in the ancestral-type diploid species Xenopus tropicalis. However, we detected lower levels of six6.S expression than six6.L expression. The six6.S enhancer sequence was more highly diverged from the orthologous enhancer of X. tropicalis than the six6.L enhancer, and showed weaker activity in a transgenic reporter assay. Based on a phylogenetic analysis of the protein sequences, we observed ...
Like most Archaea, the hypersaline-adapted organism Halobacterium salinarum exhibits characteristics from all three domains of life, including a eukaryotic histone protein, a universal propensity to genetic rearrangements, and homologs of bacterial cell division proteins. Here we investigate the ancestral function of histone protein in the Archaea. Transcriptomics, proteomics, and phenotypic assays of histone mutants determine that histone regulates gene expression and cell shape but not genome compaction in H. salinarum. We further explore the regulation of gene expression on a genome-wide scale through the study of genomic instability. Genomic deletions and duplications are detected through the meta-analysis of 1154 previously published gene expression arrays and 48 chromatin immunoprecipitation arrays. We discover that a 90 kb duplication event in the megaplasmid pNRC100 directly leads to increased gene expression, and find evidence that the chromosome is far more unstable than previously ...
PfCCp1 and PfCCp2 have similar architectures and are paralogs arising via relatively recent gene duplication after domain accretion. C. parvum also has paralogs, CpCCp1 and CpCCp2, and thus the gene duplication event likely occurred before the divergence of the apicomplexan genera. Within PfCCp1 and PfCCp2, we identified three predicted polysaccharide-binding domains, namely ricin, discoidin, and levanase-type lectin domains (26, 27). COOH terminal to these modules are two copies of an apicomplexan-specific cysteine-rich module (herein termed ApicA) that has not been identified in any other gene. Between the discoidin and levanase lectin domains there are two distinct cysteine-rich modules, the described animal- and fungal-specific LCCL domain (28), and a novel module, termed NEC, which appears in a wide range of animal proteins such as neurexins (29), fibrillar collagen α globular domain (30) from vertebrates and sponges, and the fibrinogen family of proteins (31). The NEC domain has not been ...
The globin gene superfamily as a model system. A second area of research is geared towards understanding the role of gene duplication and whole-genome duplication in the evolution of key physiological innovations. Gene duplication is thought to play an extremely important role in the evolution of novel protein and pathway functions. However, there is still much debate about the specific evolutionary mechanisms that are responsible for the initial retention and subsequent functional divergence of duplicated genes. The globin gene superfamily is an ideal model system for investigating these issues because it is one of the most intensively studied multigene families from the standpoint of molecular genetics and phylogenetic history. The globin gene families also provide an excellent example of the kind of physiological versatility that can be attained through functional and regulatory divergence of duplicated genes that encode different subunit polypeptides of the same multimeric protein. For ...
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many ...
To determine the basis for the persistence of functional gene duplicates in the genome, three scientists at the Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology in Zürich have collaborated on the largest systematic analysis of duplicated gene function to date. Using an integrative combination of computational and experimental approaches, they classified duplicate pairs of genes involved in yeast metabolism into four functional categories: (1) back-up, where a duplicate gene copy has acquired the ability to compensate in the absence of the other copy, (2) subfunctionalization, where a duplicate copy has evolved a completely new, non-overlapping function, (3) regulation, where the differential regulation of duplicates fine-tunes pathway usage, and (4) gene dosage, where the increased expression provided by the duplicate gene copy augments production of the corresponding protein.. Their results, which appear in the October issue of the journal Genome Research, ...
The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word mutation is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real ...
Comparative Genomics: Gene and Genome Duplication. What are the molecular, phenotypic, and taxonomic outcomes of gene and whole genome duplication? We use two gene families, opsins and olfactory receptors, as models to answer these questions. Most of the opsin research involves fishes including guppies, the four-eyed fish, sticklebacks, various flatfish and zebrafish. The research on olfactory receptors (ORs) involves cnidarians, sea urchins and amphioxus. Recently weve added gene duplication and cancer evolution, and gene colinearity (conserved synteny) to our research repertoire. I also co-supervise graduate students who study tube worm population genetics and protein-protein interaction networks.. ...
THE genomes of most organisms contain multiple copies of genes that are closely related in structure and function. Such gene families can arise from tandem duplications, as in the case of the HOX, hemoglobin, and keratin clusters in animals, or from polyploidization events such as those presumed to have preceded the origin of vertebrates (Ohno 1970; Morizotet al. 1991; Lundin 1993; Hollandet al. 1994; Amoreset al. 1998; Pébusqueet al. 1998), brewers yeast (Wolfe and Shields 1997; Seoighe and Wolfe 1998), and many plant species (Lewis 1979). The mechanism that preserves a large proportion of duplicate genes for long time periods, however, is unclear. The classical model predicts that duplicate genes initially have fully overlapping, redundant functions, such that one copy may shield the second copy from natural selection, if gene dosage is not critical. Because deleterious mutations occur much more frequently than beneficial mutations (Lynch and Walsh 1998), the classical model predicts that ...
Analysis of genomes shows that many gene copies are found lying next to each other, linked head to tail in an arrangement called a tandem repeat. This may occur because of errors of the normal recombination machinery that is responsible for DNA repair and crossing over during meiosis. Tandem repeats are susceptible to amplification, which is the further increase in the number of copies. This can occur during crossing over. Normal crossing over pairs up identical segments on homologous chromosomes, and then exchanges them. If the chromosomes each have a tandem repeat, the crossover machinery may line up incorrectly, leaving one homologue with three gene copies and one with only one. Repeating this process over ensuing generations can lead to dozens of extra gene copies.. Duplication of much larger portions of a genome is also possible, including whole chromosomes (called chromosomal aberrations) and even the entire genome (called polyploidy). In each case, the number of copies of a gene ...
Purpose: : To test for copy number variants in the CHM gene. Choroideremia (CHM) is an X-linked progressive chorioretinal degenerative disease that affects 1 in 50,000 males. CHM results from relative deficiency or absence of Rab escort protein-1 which is encoded by the CHM gene; however, the exact pathogenesis remains to be determined. Through genetic studies, we have determined that CHM can arise from partial and complete deletions, insertions, frameshifts, point mutations (missense and nonsense) and splice site mutations in the CHM gene. Methods: : Case control, non-randomized, study design. One female and eight male subjects were identified with fundus features consistent with a clinical diagnosis of CHM. In all cases, previous sequencing of the coding region and adjacent intronic splice sites had not found a mutation. We designed a multiplex ligation-dependent probe amplification (MLPA) assay kit for the detection of copy number variants in the CHM gene. Using this MLPA assay, we tested the ...
Failure to Diagnose Chromosome 12q duplication syndrome including overlooked symptoms and complications for under-diagnosed medical conditions.
Spinal Muscular Atrophy (SMA) is the second most common autosomal recessive genetic disorder with a 1:50 carrier frequency. Deletion /duplication change...
An understanding of the factors favoring the maintenance of duplicate genes in microbial genomes is essential for developing models of microbial evolution. A genome-scale flux-balance analysis of the metabolic network of Saccharomyces cerevisiae has suggested that gene duplications primarily provide increased enzyme dosage to enhance metabolic flux because the incidence of gene duplications in essential genes is no higher than that in nonessential genes. Here, we used genome-scale metabolic models to analyze the extent of genetic and biochemical redundancy in prokaryotes that are either specialists, with one major mode of energy generation, or generalists, which have multiple metabolic strategies for conservation of energy. Surprisingly, the results suggest that generalists, such as Escherichia coli and Bacillus subtilis, are similar to the eukaryotic generalist, S. cerevisiae, in having a low percentage (,10%) of essential genes and few duplications of these essential genes, whereas metabolic ...
This study has systematically evaluated the total pool of genomic mutations arising in 737 E. coli lines subjected to daily single-cell bottlenecks for 1−2 mo. After WGS, we detected thousands of mutational events, including point mutations, indels, prophage deletions, and large duplications, as well as their responses to sublethal concentrations of norfloxacin with or without the presence of DNA repair systems such as MMR and DNA oxidative-damage repair. Our findings demonstrate the power and resolution of MA techniques for ascertaining the consequences of exogenous factors for replication fidelity and damage repair, paving the way for future work on the mutagenic consequences of other antibiotics and other means of microbial intervention.. Numerous checks on the nature of mutations accumulated in this MA setting indicate that this experimental design cleanly separates the response of the mutation rate to antimicrobial dosage from the downstream issue of which specific mutations confer ...
Background Great gene figures in herb genomes reflect polyploidy and major gene duplication events. into paralogous protein families respectively. Singleton and paralogous family genes differed substantially in their likelihood of encoding a protein of known or putative function; 26% and Ritonavir 66% of singleton genes compared to 73% and 96% of the paralogous family genes encode a known or putative protein in rice and Arabidopsis respectively. Furthermore a major skew in the distribution of specific gene function was observed; a total of 17 Gene Ontology groups in both rice and Arabidopsis were statistically significant in their differential distribution between paralogous family and singleton proteins. In contrast to mammalian organisms we found that duplicated genes in rice and Arabidopsis tend to have more alternate splice forms. Using data from Massively Parallel Signature Sequencing we show that a significant portion of the duplicated genes in rice show divergent expression although a ...
The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. DiagHunter works efficiently with diverse, large datasets to predict extended and interrupted synteny blocks and to generate graphical and text output quickly. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity.
As part of our mission, Dup15q Alliance seeks to unite families, researchers, and professionals; and promote research, awareness, and understanding of chromosome 15q11.2-13.1 duplication syndrome and related disorders. Dup15q Alliance formally endorses and funds research and collaborates with researchers interested in research on chromosome 15q duplications by disseminating research information and promoting opportunities for Dup15q Alliance families to participate in research studies.. ...
Authors: Dearborn DC, Gager AB, McArthur AG, Gilmour ME, Mandzhukova E, Mauck RA.. Mol Ecol. 2016 Sep;25(17):4355-67.. Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defence, which in turn can select for MHC-disassortative mate choice. However, many species lack this expected pattern of MHC-disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus-specific primers for high-throughput sequencing of two expressed MHC Class II B genes in Leachs storm-petrels, Oceanodroma leucorhoa, and found that exon 2 alleles fall into two gene-specific monophyletic clades. We tested for disassortative vs. random mating at these two functionally diverged Class II B genes, using multiple metrics and different subsets of exon 2 sequence data. With good ...
Lara-Gonzalez,S. Estrella-Hernandez,P. Ochoa-Leyva,A. Portillo-Tellez,M.C. Caro-Gomez,L.A. Figueroa-Angulo,E.E. Salgado-Lugo,H. Miranda-Ozuna,J.F. Ortega-Lopez,J. Arroyo,R. Brieba,L.G. Benitez-Cardoza,C.G. 2014. Structural and thermodynamic folding characterization of triosephosphate isomerases from Trichomonas vaginalis reveals the role of destabilizing mutations following gene duplication Proteins: Structure, Function and Bioinformatics, 82, 22-33 * ...
The present study illustrates several striking features of the genetic diversity present in domestic animals. Firstly, the R2 allele exemplifies the evolution of alleles by two or more consecutive mutations. Other examples include the Dominant white allele in pigs which involves a 450 kb duplication encompassing the entire KIT gene combined with a splice mutation in one of the duplicated copies [31] and black spotting in pigs which is determined by the combined effects of two mutations in MC1R, a missense mutation associated with black colour and a somatically unstable two base-pair insertion [32]. Secondly, it represents a new example of how structural rearrangements have contributed to rapid phenotypic evolution observed in domestic animals [33], [34]. The majority of the structural changes reported to be associated with phenotypic effects, like the effects of R1 and R2 on comb morphology, constitute cis-acting regulatory mutations. The altered configurations of regulatory elements on the ...
NIH Rare Diseases : 50 16p11.2 duplication is a chromosomal change in which a small amount of genetic material within chromosome 16 is abnormally copied (duplicated). this duplication occurs in the short (p) arm of chromosome 16 at a position known as 11.2. signs and symptoms can vary widely among affected individuals. some individuals have no symptoms while others may have features such as low weight; small head size; behavioral problems; features of autism spectrum disorder; developmental delay; intellectual disability; and speech and language delays. this condition can occur sporadically as a de novo mutation (by chance) or can be inherited in an autosomal dominant manner from a parent. treatment depends on signs and symptoms present in each individual. last updated: 9/12/2016 ...
Molecular evolution Gene duplication Gene conversion Pseudogenes Ancestral gene resurrection Bovinae Ribonuclease A ENCODE ... Among different models that exist, one model suggests that after the gene duplication, among the two copies of genes, one will ... Gene conversion is of two types - interallelic and interlocus gene conversions. The resurrection of seminal RNase gene function ... Ohno, S. (1970). Evolution by gene duplication. NY: Springer. ISBN 0-04-575015-7. Benner, S.A (1990). Bioorganic Chemistry ...
Evolution by Gene Duplication. London: Allen and Unwin, ISBN 0-04-575015-7. Watson JM, Riggs A, Graves JA (1992). "Gene mapping ... Second, for individual gene loci, a number of X-linked genes are common through mammalian species. Examples are found in ... Genes on the long arm of the human X are contained in the monotreme X and genes on the short arm of the human X are distributed ... and plasma thromboplastin component gene (PTC or Factor IX). Moreover, no instances were found where an X-linked gene in one ...
A Continuation of Spetner v. Max - discusses the B-cell hypermutation model; role of gene duplication; interpretations of the ... and gene families as examples of duplication, mutation and selection. a review of Lee Spetner's "NOT BY CHANCE!" by Gert ... Spetner, L. M. (1970). "Natural selection versus gene uniqueness". Nature. 226 (5249): 948-949. Bibcode:1970Natur.226..948S. ...
Maeda N, Yang F, Barnett DR, Bowman BH, Smithies O (1984). "Duplication within the haptoglobin Hp2 gene". Nature. 309 (5964): ... Erickson LM, Kim HS, Maeda N (1993). "Junctions between genes in the haptoglobin gene cluster of primates". Genomics. 14 (4): ... Maeda N (1985). "Nucleotide sequence of the haptoglobin and haptoglobin-related gene pair. The haptoglobin-related gene ... the latter one having arisen due to the partial duplication of Hp1 gene. Three genotypes of Hp, therefore, are found in humans ...
Guillemette C, Lévesque E, Harvey M, Bellemare J, Menard V (2010). "UGT genomic diversity: beyond gene duplication". Drug Metab ...
Although Gottlieb did much pioneering work on gene duplication in polyploids, he also pioneered studying gene duplication in ... Gottlieb applied gene duplications in determining the phylogeny of "Clarkia", because "Duplications originating by chromosomal ... by one or two nuclear genes controlling the cytosolic PGI and one nuclear gene controlling the plastid PGI. The cytosolic genes ... By far the majority of Gottlieb's gene duplication work was done with PGI in Clarkia, though he also compared the PGI from the ...
Chromosome 17q12 duplication syndrome is a protein in humans that is encoded by the DUP17Q12 gene. "Entrez Gene: Chromosome ... 17q12 duplication syndrome". Retrieved 2013-02-16. CS1 maint: discouraged parameter (link) v t e. ...
Gottlieb, L. D.; Weeden, N. F. (1979). "Gene duplication and phylogeny in Clarkia". Evolution. 33 (4): 1024-1039. doi:10.2307/ ... Odrzykoski, I. J.; Gottlieb, L. D. (1984). "Duplication of genes coding 6-phosphogluconate dehydrogenase in Clarkia(Onagraceae ... Gene exchange between species must be restricted if they are to maintain genetic integrity, but, as we have seen, such ... A by-product of this accumulation of structural rearrangements has been the establishment of strong barriers to gene exchange ...
Gene duplication is the process by which a region of DNA coding for a gene is duplicated. This can occur as the result of an ... Similar to gene duplication, whole genome duplication is the process by which an organism's entire genetic information is ... That is, after duplication of genes they often change their expression pattern, for instance by getting expressed in another ... Gene coding regions have been shown to have a higher GC-content and the longer the gene is, the greater the percentage of G and ...
"Duplication within the haptoglobin Hp 2 gene". Nature. 309 (5964): 131-135. Bibcode:1984Natur.309..131M. doi:10.1038/309131a0. ...
"Duplication within the haptoglobin Hp 2 gene". Nature. 309 (5964): 131-135. Bibcode:1984Natur.309..131M. doi:10.1038/309131a0. ... and they discovered the different alleles of the HP gene that change how haptoglobins bind to free hemoglobin She received the ... Oliver Smithies and she showed that variations in haptoglobins were due to polymorphisms in the HP gene. Barbara Hyde Bowman ...
Frequent insertions, deletions, changes in the order and number of genes, and segmental duplications near gaps, centromeres and ... If two genes were the same, they were presumed to be the original gene. The chimpanzee and human genome diverged 6 million ... The macaque gained 1,358 genes by duplication.[citation needed]Triangulation of human, chimpanzee, and macaque sequences showed ... and contractions of gene families. "The goal is to reconstruct the history of every gene in the human genome," said Evan ...
Both gene duplication and lateral gene transfer have the capacity to bring about relatively large changes that are saltational ... Serres, M. H.; Kerr AR, McCormack TJ, Riley M. (2009).Evolution by leaps: gene duplication in bacteria. Biology Direct 4: 46. ... ISBN 0262600692 Serres, M. H.; Kerr, A. R.; McCormack, T. J.; Riley, M. (2009). Evolution by leaps: gene duplication in ... Freeling, M. (2009). Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or ...
In some gene families, this process is very fast, caused by random events of gene duplication and gene deletion and generates ... Recent molecular data indicate that many sets of interacting genes such as Hox genes, immunoglobulin genes, and histone genes ... gene duplication, and gene inactivation, he predicted that higher organisms contain a large number of duplicate genes and ... Nei, M (1969). "Gene duplication and nucleotide substitution in evolution". Nature. 221 (5175): 40-42. Bibcode:1969Natur.221... ...
... gene duplication, lateral gene transfer, and transposable elements (jumping genes). The neutral theory of molecular evolution, ... ISBN 978-0-632-04708-6 Serres, M. H.; Kerr, A. R.; McCormack, T. J.; Riley, M. (2009). "Evolution by leaps: gene duplication in ... In modern epigenetics, biologists observe that phenotypes depend on heritable changes to gene expression that do not involve ... doi:10.1111/j.1502-3931.1989.tb01332.x. Wagner, Günter P., Homology, Genes, and Evolutionary Innovation. Princeton University ...
She is also known for her studies on gene expression of phototransduction proteins, duplication events in opsin genes, the ... Her studies have also sought to elucidate the role and emergence of double gene duplication events in opsin protein expression ... As Briscoe herself has addressed, gene duplication and mutation events in opsins more broadly account for a large fraction of ... Briscoe, A. D. (2001). "Functional diversification of lepidopteran opsins following gene duplication". Molecular Biology and ...
Ohno S, Wolf U, Atkin NB (2009-09-02). "Evolution from fish to mammals by gene duplication". Hereditas. 59 (1): 169-87. doi: ... Gene. 757: 144949. doi:10.1016/j.gene.2020.144949. ISSN 0378-1119. PMID 32679290. Spiga F, Zhao Z, Lightman SL (March 2020). " ... "Entrez Gene: Melanocortin 2 receptor accessory protein". Metherell LA, Chapple JP, Cooray S, David A, Becker C, Rüschendorf F, ... MRAP is thought to be originated as a result of R2 genome duplication event. MRAP was found to mainly regulate the surface ...
These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in ... Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by ... Mutations in genes can have no effect, alter the product of a gene, or prevent the gene from functioning properly or completely ... Large-scale mutations in chromosomal structure include: Amplifications (or gene duplications) or repetition of a chromosomal ...
Retrieved 2014-12-11.CS1 maint: DOI inactive as of January 2021 (link) Hurles, Matthew (July 13, 2004). "Gene Duplication: The ... Gene flow involves the exchange of genes between populations and between species. The presence or absence of gene flow ... Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer ... This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors. For ...
Susumu Ohno, Author of "Evolution by gene duplication". Ph. D. in Veterinary Science in 1949. Hirohide Hamashima, Director of ...
"Venom evolution through gene duplications". Gene. 496 (1): 1-7. doi:10.1016/j.gene.2012.01.009. PMID 22285376. GBD 2013 ... Snake venom may have originated with duplication of genes that had been expressed in the salivary glands of ancestors. Venom is ... Extensive research on platypuses shows that their toxin was initially formed from gene duplication, but data provides evidence ... "Restriction and Recruitment-Gene Duplication and the Origin and Evolution of Snake Venom Toxins". Genome Biology and Evolution ...
Wong ES, Belov K (March 2012). "Venom evolution through gene duplications". Gene. 496 (1): 1-7. doi:10.1016/j.gene.2012.01.009 ... Therefore, conotoxins genes experience less selection against mutations (like gene duplication and nonsynonymous substitution ... thus cone snails are under constant selective pressure to maintain polymorphism in these genes because failing to evolve and ... "Adaptive radiation of venomous marine snail lineages and the accelerated evolution of venom peptide genes". Ann. N. Y. Acad. ...
Ohno S (1970). Evolution by Gene Duplication. New York: Springer-Verlag. ISBN 0-04-575015-7. Hardie DC, Gregory TR, Hebert PD ( ... An example for this is the deletion of recF, gene required for the function of recA, and its flanking genes. One of the ... Evidence of the deletion of the function of repair and recombination is the loss of the gene recA, gene involved in the ... probably as a result of its inclusion in Susumu Ohno's influential book Evolution by Gene Duplication, published in 1970. With ...
... this gene and SULT1A4 arose from a segmental duplication. This gene is the most centromeric of the four sulfotransferase genes ... Exons of this gene overlap with exons of a gene that encodes a protein containing GIY-YIG domains (GIYD1). Three alternatively ... The gene structure (number and length of exons) is similar among family members. This gene encodes a phenol sulfotransferase ... Two mRNA species issued from a single gene". J. Biol. Chem. 269 (45): 28200-5. PMID 7961757. Veronese ME, Burgess W, Zhu X, ...
Gossmann TI, Schmid KJ (October 2011). "Selection-driven divergence after gene duplication in Arabidopsis thaliana". Journal of ... Sex-biased genes are genes with expression exclusive to one sex and provide a potential means of rapid evolution in a species. ... Male and female sex-biased genes of A. thaliana have major differences in expression and function. Male genes expressed in the ... On the other hand, approximately 196 genes have been identified to associate with the female gametophyte. The genes identified ...
"Frequent occurrence of CYP2D6 gene duplication in Saudi Arabians". Pharmacogenetics. 7 (3): 187-91. doi:10.1097/00008571- ... Annotated PGx Gene Information for CYP2D6 Human CYP2D6 genome location and CYP2D6 gene details page in the UCSC Genome Browser ... 2010). "CYP2D6 gene variants: association with breast cancer specific survival in a cohort of breast cancer patients from the ... "Entrez Gene: CYP2D6 cytochrome P450, family 2, subfamily D, polypeptide 6". Dinama O, Warren AM, Kulkarni J (August 2014). "The ...
Natural gene duplication plays a major role in evolution. It is also implicated in several forms of human cancer including ... Amplification of the genes encoded by these amplicons generally increases transcription of those genes and ultimately the ... or naturally through gene duplication. In this context, amplification refers to the production of one or more copies of a ... This works similarly in the fungal domain with the 18S rRNA gene as well as the ITS1 non-coding region. Irrespective of the ...
The family evolved via two separate gene duplication events. The initial duplication gave rise to two genes one of subsequently ... The second duplication appears to have occurred via an unequal crossing over event. The GypA gene itself consists of 7 exons ... The MiV and MiV(J.L.) genes are arranged in the same 5' alpha-delta 3' frame whereas Sta gene is in a reciprocal 5'delta-alpha ... Kudo S, Fukuda M (1989). "Structural organization of glycophorin A and B genes: glycophorin B gene evolved by homologous ...
Max EE, Battey J, Ney R, Kirsch IR, Leder P (Jun 1982). "Duplication and deletion in the human immunoglobulin epsilon genes". ... Ig epsilon chain C region is a protein that in humans is encoded by the IGHE gene. "Human PubMed Reference:". National Center ... "Entrez Gene: IGHE immunoglobulin heavy constant epsilon". CS1 maint: discouraged parameter (link) Venkitaraman AR, Williams GT ... Ellison J, Buxbaum J, Hood L (1983). "Nucleotide sequence of a human immunoglobulin C gamma 4 gene". DNA. 1 (1): 11-8. doi: ...
Mekalanos JJ (1983). "Duplication and amplification of toxin genes in Vibrio cholerae". Cell. 35 (1): 253-63. doi:10.1016/0092- ... His early work as an independent researcher led to the identification of toxR, a gene that affects the expression of the ... the demonstration of the presence of duplications of the toxin operon in different strains of Vibrio cholerae that could ...
... greatly facilitating the evolutionary studies of gene regulation after gene duplication or speciation. Gene duplications can ... The gene duplication rate in C. elegans is on the order of 10−7 duplications/gene/generation, that is, in a population of 10 ... Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is ... It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of ...
Gene duplication has played an important role in the history of the human genome and the genomes of ancestors. Gene duplication ... The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major ... Therefore, this mechanism of gene duplication does not contribute largely to the total observed duplicated genes or gene ... A collection of human genes that have known functions have been examined for a history of gene duplications detected by means ...
... the role of duplication in chromosomal repatterning, and the role of gene duplication in reproductive isolation between species ... melanogaster genome appear to have arisen by gene duplication (6). Thus, some 34% of the fly genome, or 4624 genes [40% × 85 ... "the fate awaiting most gene duplications appears to be silencing rather than preservation," and, hence, that "duplicate genes ... Thus, figure 2 of (1) should be viewed with caution as a description of the age distribution of gene duplications. A related ...
Evolution by gene duplication is an event by which a gene or part of a gene can have two identical copies that can not be ... The first step is gene duplication. The gene duplication in itself is neither advantageous, nor deleterious, so it will remain ... of a gene duplication and its long-term outcomes. Since a gene duplication occurs in only one cell, either in a single-celled ... increases in gene expression by promoter mutations and increases in gene copy number by gene duplication[citation needed]. The ...
... and gene duplication provided an opportunity for one of the two redundant genes to evolve into the ECP gene specializing in ... has suggested that the ECP and EDN genes were produced by tandem gene duplication from an EDN-like ancestral gene after ... Positive Darwinian selection after gene duplication in primate ribonuclease genes. Jianzhi Zhang, Helene F. Rosenberg, ... Positive Darwinian selection after gene duplication in primate ribonuclease genes. Jianzhi Zhang, Helene F. Rosenberg, ...
... binary gene trees and a rooted, binary species tree, determines a minimum number of... ... Species Tree Gene Duplication Gene Tree Duplication Event Gene Duplication Event These keywords were added by machine and not ... determines a minimum number of locations for gene duplication events from the gene trees on the species tree. We examined the ... However, error in gene trees can produce erroneous evidence of large-scale duplication events, especially near the root of the ...
After the duplication: gene loss and adaptation in Saccharomyces genomes.. Cliften PF1, Fulton RS, Wilson RK, Johnston M. ... cerevisiae genes are depicted in blue with blue lines connecting paralogous gene pairs. Red lines connect orthologous gene ... Comparison of an othologous duplication block in S. cerevisiae and S. castellii. S. castellii genes (in purple) are labeled ... Analyses of the duplication regions of the genomes indicate that most of the duplicated genes (approximately 85%) were lost ...
GENE redundancy is common. It is produced by duplication of individual genes, by duplication of large chromosomal segments ( ... and by duplication of whole genomes. Gene duplications play a major role in evolution by providing paralogous genes that can ... genes, ferric iron uptake (FIT) genes, genes encoding ferric reductases (FRE), and COS and PAU (seripauperin) genes of unknown ... S. castellii, but not S. kluyveri, underwent a genome duplication:. To determine the extent of gene duplication in S. kluyveri ...
Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive ... We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In ... Yet during the actual gene-duplication process, a pre-existing gene is merely copied, and nothing truly new is generated. As ... Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this ...
... noted that the gene duplication of Mexican cavefish LWS/MWS genes, which led to R007 and an ancestral gene of G101 and G103, ... The tree strongly suggests that gene duplication leading to an ancestral gene of zebrafish RH2-1 and RH2-2 and of RH2-3 and RH2 ... Gene duplications of zebrafish opsins: It has been suggested that a genome-wide duplication occurred at the base of the teleost ... Besides LWS/MWS genes of higher primates, gene duplications in the five groups of visual opsins have been documented only for ...
13.6: Gene Duplication and Divergence The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence ... In addition to gene duplications, large-scale chromosome duplications or whole-genome duplications also occur. Some chromosomes ... Gene duplication is a process where a DNA region coding for a gene duplicates, making additional copies of itself within the ... Generation of Duplicate genes. Gene duplication can arise due to the following four reasons. First, the unequal crossing over ...
Bergman Proponents of the gene-duplication hypothesis of evolution argue that a mutation can cause the duplication of a gene ... Does gene duplication provide the engine for evolution? by Jerry ... that allows one copy of the gene to mutate and evolve to per... ... Gene duplication can involve not only whole genes, but also parts of genes, several genes, parts of a chromosome, or even ... genes are assumed to have arisen by gene duplication, a clear lack of evidence exists for gene duplication as the source of ...
... loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before the duplication ... To learn more about the evolutionary effects of the duplication event, we compa … ... The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive ... After the duplication: gene loss and adaptation in Saccharomyces genomes Genetics. 2006 Feb;172(2):863-72. doi: 10.1534/ ...
Gene duplication is one of the major drivers of the evolution of gene and protein networks. However, specific examples of how ... Gene duplications are an important source of new genes, and a variety of models have been developed to rationalize why certain ... Most models of gene duplication assume that the ancestral functions of the preduplication gene are independent and can ... E) After the duplication of AncMADS, α-specific genes are regulated by a homodimer of AncMcm1, whereas ARG genes are regulated ...
Gene duplication and subsequent evolutionary divergence certainly adds to the size of the genome and in large measure to its ... the causal sufficiency of gene duplication and subsequent divergence to account for the origin of novel biological information ... this means that the same tryspinogen-like gene could not have been the ancestral gene in this case. Although this is passed off ... Either way, the gene would seem to contribute to greater fecundity.. As it turns out, however, it is the loss of over 100 ...
Gene Duplication*. Genes, Insect. Lepidoptera / chemistry*, genetics. Light. Likelihood Functions. Molecular Sequence Data. ... Two recent opsin gene duplication events were found within the papilionid but not within the nymphalid butterfly families ... An elevated rate of evolution was detected in the red-shifted Papilio Rh3 branch following gene duplication, because of an ... 11911926 - Screening and characterization of aldehyde dehydrogenase gene from halomonas salina str.... 1971156 - Pili (fimbriae ...
Prion gene syntenies in other species. References. Duplications of the prion gene. webmaster 5 Dec 98 The hox genes [that ... Historic duplications of the prion gene. Human-mouse prion gene synteny relationships. ... Postlethwait showed earlier that gene duplications commonly split or specialize the original gene functions rather than result ... The gene structure for chicken CP49 gene is presented. It differs from the human CP49 gene with the presence of an extra exon ...
Grapevine Gene duplication Genome expansion Evolution Gene family Electronic supplementary material. The online version of this ... Thus, gene duplication and genome expansion are common in this genome. In this study, we identified 17,922 duplicated genes in ... Supplementary Table 1 Duplication types for all grapevine genes. The names of genes are given according to the 12− V. vinifera ... On the basis of this study, we believe that uncovering the underlying rules for gene duplications, expansions of gene families ...
Patient 3 is the only case we present with a chimeric gene due to an inherited duplication. As in patient 1, the fusion gene ... Deletions and duplications are usually pathogenic when affecting dose-sensitive genes. Alternatively, a chimeric gene may also ... Chimeric Genes in Deletions and Duplications Associated with Intellectual Disability. Sonia Mayo, Sandra Monfort, Mónica ... D. T. Jones, S. Kocialkowski, L. Liu et al., "Tandem duplication producing a novel oncogenic BRAF fusion gene defines the ...
... gene duplication include Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 ... Agrobacterium-Mediated Virus-Induced Gene Silencing Assay In Cotton, In situ Protocol for Butterfly Pupal Wings Using ... Ubiquitin Ligase Gene Family in Grapevine, High-throughput Functional Screening using a Homemade Dual-glow Luciferase Assay ... Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a ...
Chromosomal Translocation and Segmental Duplication in Cryptococcus neoformans James A. Fraser, Johnny C. Huang, Read Pukkila- ...
Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana.. Allen E1, Xie Z, ... Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. ... Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA-generating loci possess the ... We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target ...
The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD ... Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database BMC Genomics. 2016 May 18;17: ... Keywords: Assembly; Gar; Gene duplication; Gene expression; Holostean; Mcam; Salmonids; Stra8; Teleosts. ... The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD ...
SNP/CGH array analysis in this family demonstrated in both siblings a biallelic duplication inherited from the heterozygous ... parents, disrupting the ADGRB3 gene. ADGRB3, also known as BAI3, belongs to the subfamily of adhesion G protein-coupled ... findings further support this association and also suggest that biallelic variants affecting the function of the ADGRB3 gene ... Scuderi, C., Saccuzzo, L., Vinci, M. et al. Biallelic intragenic duplication in ADGRB3 (BAI3) gene associated with intellectual ...
In one AML, insertion and deletion without duplication was determined. All 24 lengthened sequences were in-frame. Duplication ... The sequence analysis of the abnormal PCR products revealed that 23 of 24 showed internal tandem duplication with or without ... examined a large number of patients to clarify the distribution and frequency of a recently described FLT3 tandem duplication ... Internal tandem duplication of the FLT3 gene is preferentially seen in acute myeloid leukemia and myelodysplastic syndrome ...
... is important for maintaining rapid chromosome duplication. Furthermore, RecA and RecBCD together can sustain viability in the ... in both bacteria and lower eukaryotes but how these replication repair systems interact to ensure efficient genome duplication ... of replisome pausing by accessory helicases has a more significant impact on successful completion of chromosome duplication ... Recombination enzymes also aid genome duplication by facilitating the repair of DNA lesions via strand exchange and also ...
SherbakovAbstractThe evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, ... Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that ... Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. *. ... SherbakovAbstractThe evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, ...
Posted in Publications , Tagged deep coalescence, gene duplication and loss, gene tree, homology categories, horizontal gene ... loss forensic genetics gene duplication and loss gene family gene tree genome grants HIV-1 homology categories horizontal gene ... Tag Archives: gene duplication and loss. Unsorted Homology within Locus and Species Trees. Posted on October 14, 2014 by dmallo ... cabo verde cancer cancer evolution cape verde conus deep coalescence duplication and ...
"The Replication Fork: Understanding the Eukaryotic Replication Machinery and the Challenges to Genome Duplication." Genes 4, no ... Understanding the Eukaryotic Replication Machinery and the Challenges to Genome Duplication. Genes 2013, 4, 1-32. ... Understanding the Eukaryotic Replication Machinery and the Challenges to Genome Duplication. Genes. 2013; 4(1):1-32. ... Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert ...
Anti-longevity-associated gene families have significantly increased rate of duplication compared to pro-longevity gene ... Many longevity-associated pathways evolved via gene duplication, and duplication can increase lifespan and impact the ... Gene Duplication and the Evolution of Longevity in Mammals. Permalink No Comments Yet Add a Comment Posted by Reason ... Gene duplication is often the key to understanding the origin and evolution of important Eutherian phenotypes. ...
  • Comparisons of genomes demonstrate that gene duplications are common in most species investigated. (wikipedia.org)
  • It is well known that gene duplication has been a major process in the evolution of genomes. (pnas.org)
  • Gene duplication has played an important role in the history of the human genome and the genomes of ancestors. (pnas.org)
  • Their analysis led to several interesting observations, particularly with respect to the rate of gene duplication in eukaryotic genomes and the subsequent half-life of duplicates. (sciencemag.org)
  • The underlying mutational event of duplication may be a conventional gene duplication mutation within a chromosome, or a larger-scale event involving whole chromosomes (aneuploidy) or whole genomes (polyploidy). (wikipedia.org)
  • Such non-functional remnants of genes, with detectable sequence homology, can sometimes still be found in genomes and are called pseudogenes. (wikipedia.org)
  • After the duplication: gene loss and adaptation in Saccharomyces genomes. (nih.gov)
  • The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before the duplication event. (nih.gov)
  • To learn more about the evolutionary effects of the duplication event, we compared the S. cerevisiae genome to other Saccharomyces genomes. (nih.gov)
  • Analyses of the duplication regions of the genomes indicate that most of the duplicated genes (approximately 85%) were lost before the speciation. (nih.gov)
  • It is produced by duplication of individual genes, by duplication of large chromosomal segments (segmental duplication), by duplication of entire chromosomes (aneuploidy), and by duplication of whole genomes. (genetics.org)
  • Study of intrachromosomal duplications among the eukaryote genomes. (biomedsearch.com)
  • The coexistence of divergent groEL/cpn60 genes in different genomes in one cell offers insights into gene transfer from evolving chloroplasts to cell nuclei and convergent gene evolution in chlorophyll a/b versus chlorophyll a/c/phycobilin eukaryotic lineages. (nih.gov)
  • SherbakovAbstractThe evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). (medworm.com)
  • Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. (medworm.com)
  • Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding. (medworm.com)
  • The majority of remolded tRNA genes (seven out of ten cases) were found in the mt genomes of endemic amphipod species from Lake Baikal. (medworm.com)
  • The possible reasons for the unusual abundance of additional tRNA genes in the mt genomes of Baikalian amphipods are discussed.The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional case. (medworm.com)
  • Researchers here use some of the more recently sequenced mammalian genomes , of the majority eutherian branch that encompasses all of the mammals you might be familiar with, to investigate a potential role for gene duplication in the evolution of aging and longevity. (fightaging.org)
  • With the availability of genomes from long- and short-lived species and a set of hundreds of genes known to influence lifespan in model organisms, we thoroughly investigated the role that gene duplication played in the evolution of Eutherian longevity from a systematic perspective. (fightaging.org)
  • These two processes result in different loci, across a set of related genomes, having different gene trees. (rice.edu)
  • Inferring the phylogeny of the genomes from data sets of such gene trees is a central task in phylogenomics. (rice.edu)
  • Furthermore, when the evolutionary history of the genomes includes relatively close divergence events, as in cases of closely related organisms or rapid radiations, deep coalescence of gene copies could be at play, in addition to duplication and loss, further adding to the complexity of gene/genome relationships. (rice.edu)
  • Plant genomes are prone to duplication and paralogs are particularly widespread in the floral organ identity genes. (washington.edu)
  • Tests of hypotheses using analyses of complete genomes, interpreted in a phylogenetic context, provide evidence regarding the relative importance of gene duplication. (indigo.ca)
  • In search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. (biomedcentral.com)
  • Whole-genome sequencing of clinical isolates recently established that some P. vivax genomes contain two copies of the PvDBP gene. (harvard.edu)
  • Overall, this analysis emphasises the potential for a richly diversified clock gene network to serve a mixture of circadian and non-circadian functions in vertebrate groups with complex genomes. (prolekare.cz)
  • Single gene duplications are prevalent even in eukaryotes with small genomes. (utexas.edu)
  • Here, we present a genome-wide survey of the genes encoding these enzymes, KCS genes, in 28 species (26 genomes and two transcriptomes), which represents a large phylogenetic scale, and also reconstruct the evolutionary history of this gene family. (springer.com)
  • The zebrafish genome possesses 2 jak2 genes that occupy paralogous chromosome segments in the zebrafish genome, and these segments conserve syntenic relationships with orthologous genes in mammalian genomes, suggesting an ancient duplication in the zebrafish lineage. (epfl.ch)
  • How genes evolve after genome duplication is thus a crucial question to understand the mechanisms by which genomes evolved and drive vertebrate development and physiology. (anr.fr)
  • When we compared the genomes of apes and humans, we found that the humans had evolved complex structural changes at 16p11.2 associated with deletions and duplications that often result in autism. (conductdisorders.com)
  • With the increase in numbers of sequenced plant genomes, synteny analysis can provide new insights into gene family evolution. (plantcell.org)
  • Specifically, we analyzed synteny networks of the MADS-box transcription factor gene family using 51 completed plant genomes. (plantcell.org)
  • Conserved gene order can be retained for hundreds of millions of years and provides critical information about conserved genomic context and the evolution of genomes and genes. (plantcell.org)
  • Additional searching of the genomes of two other mosquito species led to the discovery of four Cht5-like genes in Aedes aegypti and three in Culex quinquefasciatus. (k-state.edu)
  • Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. (semanticscholar.org)
  • Comparison of these genomes at single base pair level has suggested the presence of a mechanism for bacterial gene mobility--insertion with long target duplications. (semanticscholar.org)
  • Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes. (semanticscholar.org)
  • Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. (semanticscholar.org)
  • The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. (pacb.com)
  • For example, chromosomal recombination can result in the loss of a gene on one chromosome and the gain of an extra copy on the sister chromosome. (creation.com)
  • Gene duplication can involve not only whole genes, but also parts of genes, several genes, parts of a chromosome, or even entire chromosomes. (creation.com)
  • If it were not for subsequent gene loss (variable by chromosome and gene) over the last 420 million years, the haploid mammal or bird would have 4 copies of the prion gene , pufferfish 8 copies, and salmon 16 copies. (mad-cow.org)
  • One might think -- based on the respective locations of the prion genes -- that mouse chromosome 2 corresponds to human chromosome 20. (mad-cow.org)
  • The latest human chromosome radiation hybrid G3 map gives locations for 33,000 human genes (Deloukas, P. Science 282, 744-746, 1998. (mad-cow.org)
  • The best available location of the human prion gene seems to be 20pter12.17 or about 9,448,000 bp in from the telomere on the short arm of chromosome 20. (mad-cow.org)
  • Single nucleotide polymorphism/comparative genomic hybridization (SNP/CGH) array analysis demonstrated in both siblings a homozygous duplication of chromosome 6q12 involving the ADGRB3 (MIM 602684) gene, inherited from the heterozygous parents. (nature.com)
  • Here, we demonstrate that the DNA content defects of Escherichia coli cells lacking the strand exchange protein RecA are driven primarily by conflicts between replication and transcription, as is the case in cells lacking the accessory helicase Rep. However, in contrast to Rep, neither RecA nor RecBCD, the helicase/exonuclease that loads RecA onto dsDNA ends, is important for maintaining rapid chromosome duplication. (mdpi.com)
  • Our data indicate that the minimisation of replisome pausing by accessory helicases has a more significant impact on successful completion of chromosome duplication than recombination-directed fork repair. (mdpi.com)
  • The area that looked to be the most promising was on chromosome 6, in a region that contained a gene related to notochord development that is called the T gene or brachyury. (healthcanal.com)
  • The scientists then looked for CNVs in the region on chromosome 6 that included the T gene in DNA from seven families (65 people, including 21 chordoma patients) in which at least two blood relatives had the disease. (healthcanal.com)
  • We performed an in-depth evolutionary analysis of a region of chromosome 1, which is copy number polymorphic among humans, and that contains at least 32 PRAME (Preferentially expressed antigen of melanoma) genes and pseudogenes. (biomedcentral.com)
  • Analysis of the custom-capture NGS sequencing data for copy number variants uncovered a tandem duplication of approximately 60 kb on chromosome 6q. (molvis.org)
  • 50 16p11.2 duplication is a chromosomal change in which a small amount of genetic material within chromosome 16 is abnormally copied (duplicated). (malacards.org)
  • this duplication occurs in the short (p) arm of chromosome 16 at a position known as 11.2. (malacards.org)
  • 16p11.2 Duplication, also known as 16p11.2 duplication syndrome , is related to chromosome 16p11.2 duplication syndrome and autism spectrum disorder . (malacards.org)
  • An important gene associated with 16p11.2 Duplication is DUP16P11.2 (Chromosome 16p11.2 Duplication Syndrome). (malacards.org)
  • The duplication occurs near the middle of the chromosome at a location designated p11.2. (malacards.org)
  • The duplication was likely DNA based, as other Y-linked genes remain on the Y chromosome, the locations of introns are conserved, and expression analyses suggest that regulatory elements remain linked. (cam.ac.uk)
  • Because the dot chromosome contains seven times more genes than the Y and is exposed to selection in both males and females, these results suggest that the dot suffers the deleterious effects of genetic linkage to more selective targets compared with the Y chromosome. (cam.ac.uk)
  • Thus, a highly degenerate Y chromosome may not be the worst environment in the genome, as is generally thought, but may in fact be protected from the accumulation of deleterious mutations relative to other nonrecombining regions that contain more genes. (cam.ac.uk)
  • We have defined the relative orientation of SORD1 and SORD2 genes with respect to both the centromere and each other and established their exact chromosome location. (deepdyve.com)
  • Chromosome IV duplication is the most frequent mutation, as well as the only change in chromosomal copy number seen in the screen. (g3journal.org)
  • Using a genetic mapping strategy that involves systematically deleting segments of a duplicated chromosome, we show that the chromosome IV's duplication effect is largely due to the generation of a second copy of the stress-inducible cytoplasmic thioredoxin peroxidase TSA2 . (g3journal.org)
  • An important question regarding such conditionally beneficial aneuploidies is, do their effects tend to arise due to changes in the copy numbers of one or multiple genes on the aneuploid chromosome(s)? (g3journal.org)
  • These genes, AOP2 and AOP3 , which map to the same position on chromosome IV, result from an apparent gene duplication and control the conversion of methylsulfinylalkyl glucosinolate to either the alkenyl or the hydroxyalkyl form. (plantcell.org)
  • All of these genes are found in a single cluster on chromosome 2R. (k-state.edu)
  • Features that have been described in some people with chromosome 4q duplication include developmental delay , intellectual disability , behavioral problems, birth defects , and distinctive facial features. (malacards.org)
  • Chromosome 4q Duplication, also known as chromosome 4, trisomy 4q , is related to partial trisomy distal 4q and microcephaly . (malacards.org)
  • In males (who have only one X chromosome), a duplication of the only copy of the MECP2 gene in each cell is sufficient to cause the condition. (medlineplus.gov)
  • Females with a MECP2 gene duplication tend to be unaffected or less severely affected than males because the X chromosome that contains the duplication may be turned off (inactive) in many of their cells due to a process called X-inactivation . (medlineplus.gov)
  • Females with a MECP2 gene duplication often have skewed X-inactivation, which results in the inactivation of the X chromosome containing the duplication in most cells of the body. (medlineplus.gov)
  • Although this skewed X-inactivation ensures that the chromosome with the normal MECP2 gene is active most often, some of these females develop behavioral and psychiatric symptoms thought to be related to the additional genetic material. (medlineplus.gov)
  • It results from either a microdeletion of or a deleterious sequence variant in the gene euchromatic histone-lysine N-methyltransferase 1 ( EHMT1 ) on chromosome 9q34. (biomedcentral.com)
  • GTF2H2 gene is part of a 500 kb inverted duplication on chromosome 5q13. (antibody-antibodies.com)
  • It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. (antibody-antibodies.com)
  • 2p duplications fall into a category of chromosome disorders in which a segment of chromosome 2 is duplicated or copied. (globalgenes.org)
  • Duplications generally arise by random chance (de novo), but also can be the result of inheriting a chromosome error from the parents. (globalgenes.org)
  • Rapid evolution and functional divergence have been observed at the level of the transcription of duplicated genes, usually by point mutations in short transcription factor binding motifs. (wikipedia.org)
  • A classic view, owing to Susumu Ohno, which is known as Ohno model, he explains how duplication creates redundancy, the redundant copy accumulates beneficial mutations which provides fuel for innovation. (wikipedia.org)
  • If the amount of gene product is below its optimal level, there are two kinds of mutations that can increase dosage: increases in gene expression by promoter mutations and increases in gene copy number by gene duplication[citation needed]. (wikipedia.org)
  • However, at a later time, such mutations could still occur, leading to genes with different functions (see below). (wikipedia.org)
  • In cases of gene duplications that have no immediate fitness effect, a retention of the duplicate copy could still be possible if both copies accumulate mutations that for instance reduce the functional efficiency of the encoded proteins without inhibiting this function altogether. (wikipedia.org)
  • However, it has been controversial whether the functional divergence occurs by positive Darwinian selection that accelerates the fixation of advantageous mutations (largely nonsynonymous or amino acid-altering mutations) ( 6 ) or by random fixation of neutral mutations, which later induce a change in gene function when the environment or the genetic background is altered (Dykhuizen-Hartl effect) ( 7 , 8 ). (pnas.org)
  • Here, one of the gene paralogs may acquire deleterious mutations and turn into a nonfunctional copy called a pseudogene. (jove.com)
  • The second is sub-functionalization where both the paralogs acquire mutations in different protein coding domains or exons, thus partitioning the original gene function between them. (jove.com)
  • Here, one paralog acquires novel, advantageous mutations that can lead to the evolution of a new gene. (jove.com)
  • For example, the human β-globin gene duplicated and acquired mutations to produce a new gene called fetal β-globin that is expressed exclusively in the human fetus. (jove.com)
  • However, it will usually evolve by having its own mutations and in due time it may acquire functions that differ from those of its sister gene. (creation.com)
  • Alternatively, subfunctionalization (via the duplication-degeneration-complementation model) holds that duplicates can be maintained in the genome by acquiring reciprocal loss-of-function mutations, such that both duplicates become necessary to perform the combined functions of the preduplication ancestor ( 1 - 3 ). (sciencemag.org)
  • Usual types of gene mutations and gene duplications are permanent changes to the DNA that a person inherits from parents. (healthcanal.com)
  • Chordomas in the three families without T gene duplications may result from mutations of other genes or an as yet unidentified process involving the T gene," said Yang. (healthcanal.com)
  • After the KRAS mutation was induced by the researchers, other mutations in what are known as tumor suppressor genes developed. (medizin-aspekte.de)
  • Thus, although the initial fixation of the kl-5 duplication may have been advantageous, slightly deleterious mutations have accumulated in the dot-linked copies of kl-5 faster than in the Y-linked copies. (cam.ac.uk)
  • Through genetic studies, we have determined that CHM can arise from partial and complete deletions, insertions, frameshifts, point mutations (missense and nonsense) and splice site mutations in the CHM gene. (arvojournals.org)
  • Using this MLPA assay, we tested the DNA of those CHM patients that screened negative for mutations in the CHM gene. (arvojournals.org)
  • Moreover, beneficial single-point mutations occurring in the cis -regulatory region of the gene of interest would be mostly sufficient to face several environmental changes ( Wray, 2007 ). (elifesciences.org)
  • Mutations in the HOXA13 gene have been shown to cause hand-foot-genital syndrome (HFGS). (bmj.com)
  • This finding illustrates the minor consequences of HOX gene mutations in humans and serves as an example of dominant inheritance of hypospadias. (bmj.com)
  • 1 Mutations in the gene encoding the methyl-CpG binding protein 2 (MECP2) were demonstrated as the cause of Rett syndrome, 2 and confirmed by a number of studies. (bmj.com)
  • Both point mutations and deletions affecting the MECP2 gene have been identified in girls with this neurodevelopmental disorder. (bmj.com)
  • The high rates of gene duplication may actually facilitate the rapid evolution of gene-family members by increasing the number of opportunities for beneficial mutations to occur through increases in the gene copy number,' said Chang, a doctoral student in the Department of Ecology and Evolutionary Biology. (umich.edu)
  • Over evolutionary time, the extra copy of the gene can accumulate random mutations. (umich.edu)
  • Beneficial mutations-ones that result in a valuable new function-can be retained through natural selection, resulting in a new gene and the creation of a gene family. (umich.edu)
  • B. Some AFCP genes have mutations that allow them to perform better than others. (coursehero.com)
  • C. Some AFCP genes have mutations that prevent them from performing their function. (coursehero.com)
  • Menkes disease (MD) is an X-linked, fatal neurodegenerative disorder of copper metabolism, caused by mutations in the ATP7A gene. (biomedcentral.com)
  • To date, about 250 mutations in the ATP7A gene have been reported and are partly registered in the Human Mutation Database http://www.hgmd.org . (biomedcentral.com)
  • However, documentation of molecular changes underlying adaptive traits requires additional information about the specific genes involved and the regulatory or structural implications of the identified mutations. (biomedcentral.com)
  • Deletions and duplications are usually pathogenic when affecting dose-sensitive genes. (hindawi.com)
  • To decipher the underlying regulatory mechanisms, and thus to understand better how digits develop, we engineered a series of deletions and duplications in vivo. (epfl.ch)
  • One hypothesis is that differences among people in how the region is organized, such as the number of copies of genes like BOLA2 present and the precise locations at which deletions and duplications start and end, contribute to this variability. (conductdisorders.com)
  • We believe this work will lead to new insights about the genetic underpinnings of autism and other conditions associated with 16p11.2 deletions and duplications, potentially paving the way for more specific diagnostics and treatments for patients in the future,' Mr. Nuttle said. (conductdisorders.com)
  • The analysis showed a much richer than expected pattern of deletions and duplications of many genomic regions. (mindzilla.com)
  • http://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0009-9120&volume=&spage=&epage=&date=2005&atitle=Detecting+exon+deletions+and+duplications+of+the+DMD+gene+using+Multiplex+Ligation-dependent+Probe+Amplification+(MLPA). (hku.hk)
  • Additionally, quantitative PCR (qPCR) is used to test for the presence of large deletions and duplications of the PRKAR1A gene. (mayocliniclabs.com)
  • Deletions and duplications only. (mayocliniclabs.com)
  • Lynch and Conery ( 1 ) presented one of the first serious efforts to study the evolutionary fate of gene duplication using genomic sequence data. (sciencemag.org)
  • Knowledge of evolution by gene duplication has advanced more rapidly in the past 15 years due to new genomic data, more powerful computational methods of comparative inference, and new evolutionary models. (wikipedia.org)
  • Our algorithm can provide hypotheses for precise locations of large-scale gene duplication events with data from relatively few gene trees and can complement other genomic approaches to provide a more comprehensive view of ancient large-scale gene duplication events. (springer.com)
  • A subsequent analysis of the breakpoint regions clearly indicated a direct tandem duplication disrupting the genomic structure of the gene. (nature.com)
  • Based on their finding that duplications of the T gene cause an increased risk for chordoma in some families, the scientists suggest that future efforts to identify novel genes for familial cancers may benefit from screening for complex genomic rearrangements in addition to using traditional gene-mapping approaches. (healthcanal.com)
  • These findings highlight the genomic complexity of this species and the importance of selective gene duplications in the adaptation of fishes to challenging environment. (csic.es)
  • Comparison with a genomic segment of a pig CYP4A fatty acid hydroxylase gene ( CYP4A24 ) revealed a sequence identity with CYP4A21 that extends beyond the exons, indicating a common origin by gene duplication. (biochemj.org)
  • A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish. (biomedcentral.com)
  • Genomic data show that AtMge1 and AtMge2 arose from a recent whole-genome duplication event. (plantphysiol.org)
  • The study by Chang and Duda looked at conotoxin gene sequences from the genomic DNA of four closely related Conus species. (umich.edu)
  • We demonstrate, by gene deletion analysis, that Mre11 has a critical role in maintaining genomic integrity in Trypanosoma brucei. (lancs.ac.uk)
  • One possible explanation for the large number of gene duplication events is one or more large-scale duplications, possibly whole genome or segmental duplication(s), which provides a genomic basis for the successful radiation of early eukaryotes. (biomedcentral.com)
  • Combined, these findings provide new hypotheses for the genomic origins, biological conservation, and divergence of MADS-box gene family members. (plantcell.org)
  • By using phylogenetic and genomic analyses we show here that teleosts, unlike tetrapods, have two closely linked AQP1 paralogous genes, termed aqp1a and aqp1b (formerly AQP1o). (biomedcentral.com)
  • Array comparative genomic hybridization analysis revealed a 145 kilobases duplication spanning exons 2 to 10 of EHMT1 . (biomedcentral.com)
  • The submicroscopic duplication in EHMT1 was detected by array comparative genomic hybridization (aCGH). (biomedcentral.com)
  • The products of this recombination are a duplication at the site of the exchange and a reciprocal deletion. (wikipedia.org)
  • It thus seems that, in this case, deletion was one of the necessary factors involved in the gene fusion. (evolutionnews.org)
  • All the genes forming these fusion transcripts may have an important role in central nervous system development and/or in gene expression regulation, and therefore not only their deletion or duplication but also the resulting chimeric gene may contribute to the phenotype of the patients. (hindawi.com)
  • Interstitial deletion can also generate fusion genes as described by Tomlins et al. (hindawi.com)
  • Chimeric genes can have different possible consequences: when due to a deletion, not only the loss of a fully functional copy of the gene is especially relevant for haploinsufficient genes, but also the gain-of-function of the chimeric gene. (hindawi.com)
  • In one AML, insertion and deletion without duplication was determined. (nature.com)
  • Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping. (mindzilla.com)
  • These two parameters are of particular importance in studying the evolutionary processes of gene duplication and subsequent functional divergence. (sciencemag.org)
  • Second, the calculation of the half-life of gene duplicates was based on the untested, hidden assumption that the rate of gene duplication is constant over evolutionary time-an assumption implicit in both figure 3 and equation 3 of ( 1 ). (sciencemag.org)
  • nevertheless, there is some evidence that the duplication rate for some families may indeed not be stationary over a short evolutionary time. (sciencemag.org)
  • Assuming that small values of S may more reliably reflect a short evolutionary time, the authors chose to estimate the half-life of duplicate genes only from gene pairs with S values in the range of 0 to 0.25. (sciencemag.org)
  • Evolutionary mechanisms of origins of new gene function have been a subject of long-standing debate. (pnas.org)
  • It was also found that the number of arginine residues increased substantially in a short period of evolutionary time after gene duplication, and these amino acid changes probably produced the novel anti-pathogen function of ECP. (pnas.org)
  • Moreover, the evolutionary rates of the ECP and EDN genes, particularly the former, are among the highest of all primate genes so far studied ( 19 ). (pnas.org)
  • To learn more about the evolutionary consequences of the whole genome duplication, we investigated the fate of the duplicated genes during evolution of Saccharomyces species. (genetics.org)
  • Darwinists therefore have nothing more to go on than to depend heavily upon extrapolations from gene similarities-a circular argument founded upon the assumption of evolution, and yet another example of evolutionary story telling. (creation.com)
  • Gene duplications are an important source of new genes, and a variety of models have been developed to rationalize why certain gene duplicates have been maintained over evolutionary time ( 1 - 3 ). (sciencemag.org)
  • Analyses of the evolutionary patterns for different types of duplication using non-synonymous and synonymous substitution rates uncovered a series of underlying rules. (springer.com)
  • On the basis of this study, we believe that uncovering the underlying rules for gene duplications, expansions of gene families, and their evolutionary styles will contribute significantly to a comprehensive understanding of the features of the grapevine genome. (springer.com)
  • Gene duplication and loss are two evolutionary processes that occur across all three domains of life. (rice.edu)
  • Genes encoding transcription factors involved in intrinsic developmental control processes appear acutely sensitive to changes in gene dosage through local gene duplication, on an evolutionary time scale. (harvard.edu)
  • The alternative explanation is that the evolution of regulatory elements that control the expression of and interactions among genes has been a more important force in shaping evolutionary innovation. (indigo.ca)
  • Gene duplications are traditionally considered to be a major evolutionary source of new protein functions. (biomedcentral.com)
  • Structural and evolutionary characterization of the human sorbitol dehydrogenase gene duplication Carr, Ian M. (deepdyve.com)
  • To define the evolutionary relationship of these human genes, SORD from the marmoset was also sequenced for comparison. (deepdyve.com)
  • Gene duplication has enthralled researchers for decades due to its link to the emergence of major evolutionary innovations in organisms of ranging complexity ( Ohno, 1970 ). (elifesciences.org)
  • Hence, the loss of the new-born gene is the most common evolutionary fate. (elifesciences.org)
  • In rare occasions, this evolutionary process leads to the origin of a novel, previously unexplored function by one of the gene copies ( Conant and Wolfe, 2008 ). (elifesciences.org)
  • In modern vertebrates, these networks contain multiple copies of clock gene family members, which arose through whole genome duplication (WGD) events during evolutionary history. (prolekare.cz)
  • Gene duplication and neo-functionalization in the evolutionary and fu" by Brandon L. Logeman, L. Kent Wood et al. (unl.edu)
  • Gene and genome duplication are major sources of material for evolutionary innovations in eukaryotes that provide opportunities for novel function, increased complexity, and rapid speciation. (utexas.edu)
  • The evolutionary fate of gene duplicates has been debated since the 1970s. (utexas.edu)
  • Now, two University of Michigan evolutionary biologists report that their reconstruction of the evolutionary history of these genes has revealed rapid and continuous gene duplication over the last 11 million years that is coupled with the accelerated rates of conotoxin evolution. (umich.edu)
  • Our main result, as I see it, is that this rapid gene turnover is something that can drive rapid evolution,' said Duda, an associate professor of ecology and evolutionary biology and associate curator of the U-M Museum of Zoology. (umich.edu)
  • Gene duplication has been a ubiquitous phenomenon during eukaryotic history and has contributed to evolutionary innovation by generating additional genetic material for functional divergence and novelty [ 4 ]. (biomedcentral.com)
  • The most frequent class of duplications appeared to be similar in all six species, which suggests some silencing process for old duplicates. (sciencemag.org)
  • s problem that given a collection of rooted, binary gene trees and a rooted, binary species tree, determines a minimum number of locations for gene duplication events from the gene trees on the species tree. (springer.com)
  • However, error in gene trees can produce erroneous evidence of large-scale duplication events, especially near the root of the species tree. (springer.com)
  • Blanc, G., Wolfe, K.H.: Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. (springer.com)
  • In addition to S. castellii, other Saccharomyces sensu lato species likely diverged from S. cerevisiae after the duplication. (nih.gov)
  • A thorough analysis of these species will likely reveal other important outcomes of the whole genome duplication. (nih.gov)
  • Although rare, whole genome duplications have played a major role in the evolution of species. (genetics.org)
  • The genome of S. bayanus , a member of the sensu stricto group of Saccharomyces species, is highly similar to that of S. cerevisiae and has a high degree of synteny, indicating that it speciated after the genome duplication. (genetics.org)
  • The fate of many of the duplicated genes is different in these two Saccharomyces species, providing a view of genome evolution after a genome duplication. (genetics.org)
  • Therefore, the species which evolved after the duplication event, such as the old world monkeys, apes, and humans have three opsin genes which impart tricolor vision. (jove.com)
  • Across several species, a large number of gene families are characterized. (jove.com)
  • We show that a set of historical amino acid sequence substitutions minimized paralog interference in contemporary species and, in doing so, increased the molecular complexity of this gene regulatory network. (sciencemag.org)
  • Therefore it is important to carefully review the ever-changing status of prion gene chromosomal mapping and synteny with all possible species pairs. (mad-cow.org)
  • All additional mt tRNA genes arose independently in the Baikalian amphipods, indicating the unusual plasticity of tRNA gene evolution in these species assemblages. (medworm.com)
  • There is a cluster of longevity-associated gene families that expanded solely in long-lived species that is significantly enriched in pathways relating to 3-UTR -mediated translational regulation, metabolism of proteins and gene expression , pathways that have the potential to affect longevity. (fightaging.org)
  • The identification of a gene cluster that duplicated solely in long-lived species involved in such fundamental processes provides a promising avenue for further exploration of Eutherian longevity evolution. (fightaging.org)
  • Because we know that the environment and condition of an individual play a massive role on the proteins that are being expressed, perhaps the true meaning of the reason for duplicating these genes in long-lived species may not be fully understood from solely this perspective. (fightaging.org)
  • It is possible that duplicating a small cluster of interrelated genes solely in long-lived species that have core functions involved in RNA and protein metabolism could have directly or indirectly impacted their longevity through their functions in gene and protein networks. (fightaging.org)
  • To that end, I use the species T. thalictroides, from the clade sister to all other eudicots, with two C class gene orthologs and three B class gene orthologs. (washington.edu)
  • Comparison of transcription factor genes of C. elegans and Caenorhabditis briggsae was therefore carried out and revealed very few examples of functional gene duplication since the divergence of these species for most, but not all, transcription factor gene families. (harvard.edu)
  • Because Thalictrum lacks petals, and has lost the petal-specific AP3 , we also asked whether heterotopic expression of the remaining AP3 genes contributes to the partial transference of petal function to the first whorl found in insect-pollinated species. (frontiersin.org)
  • Here, we identify and characterize a Y to autosome duplication of the male fertility gene kl-5 that occurred during the evolution of the testacea group species of Drosophila. (cam.ac.uk)
  • Marmoset SORD, which appears to be a single gene in this species, shows significantly less homology with either SORD1 or SORD2 than they do with each other, suggesting that the human homologs represent a recent gene duplication event. (deepdyve.com)
  • Phylogenomics relationships with other fish species were established to locate temporal speciation and to assign duplication events. (csic.es)
  • The intron-exon organization of the CYP4A21 gene corresponds to that of CYP4A fatty acid hydroxylase genes in other species. (biochemj.org)
  • Phylogenetic analysis indicated that duplication and preservation of Mge s occurred independently in many plant species, which suggests a common tendency in the evolution of the genes. (plantphysiol.org)
  • Subsequently, KCS genes duplicated to generate 11 genes of angiosperm origin, expanding up to 20-30 members in further-diverged angiosperm species. (springer.com)
  • The study by Chang and Duda is the first to examine conotoxin genes from several closely related species to reconstruct the evolution of conotoxin gene families. (umich.edu)
  • Within a species, genes that are extremely similar in structure and function are considered to be part of the same gene family. (umich.edu)
  • Today, the typical cone-snail species has 100 to 200 unique neurotoxins in its venom, and the gene-duplication process likely contributed to this diversity, said Chang and Duda. (umich.edu)
  • However, the extent, role and consequences of gene duplications in the origins of ecological adaptations, especially in the context of species interactions, have been less clear. (umich.edu)
  • Syntenic relationships across a wide range of species thus provide crucial information to address fundamental questions on the evolution of gene families that regulate important developmental pathways. (plantcell.org)
  • Thus, the presence of a Cht5 gene cluster appears to be unique to mosquito species and these genes may have resulted from gene tandem duplications. (k-state.edu)
  • Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. (wikipedia.org)
  • It is unclear, however, that silent divergence is a suitable proxy for a molecular clock involving different genes or gene duplicates. (sciencemag.org)
  • This situation differs from description of divergence time using S values from homologous genes across a group of organisms, in which a dependable molecular clock may exist. (sciencemag.org)
  • In such a case, the molecular function (e.g. protein/enzyme activity) would still be available to the cell to at least the extend that was available before duplication (now provided by proteins expressed from two gene loci, instead of one gene locus). (wikipedia.org)
  • Here we report a convincing case in which positive Darwinian selection operated at the molecular level during the evolution of novel function by gene duplication. (pnas.org)
  • In this study we aimed to examine the zebrafish genome for the cone opsin genes, determine the absorption spectra of all visual pigments, and compare the expression level among opsin genes in the retina to establish the molecular basis of visual capabilities of zebrafish. (genetics.org)
  • 10 Gene duplication could not be evaluated experimentally, though, until the development of molecular biology techniques. (creation.com)
  • However, for the many gene products that participate in cooperative assemblies, the molecular interactions that underlie gene functions are not intrinsically independent ( 4 ). (sciencemag.org)
  • In these instances, loss of one or more ancestral molecular interactions will often give rise to competitive interference between gene duplicates (paralog interference) ( 5 ). (sciencemag.org)
  • The hox genes [that determine anterior-posterior axial cell fate in bilateral animals] are the most interesting thing going in molecular biology today (besides genomics). (mad-cow.org)
  • In the years since the publication of Susumu Ohno's 1970 landmark book Evolution by gene duplication tremendous advances have been made in molecular biology and especially in genomics. (indigo.ca)
  • The boundaries of the Cambodian PvDBP duplication differ from those previously identified in Madagascar, meaning that current molecular assays were unable to detect it. (harvard.edu)
  • Through a precise quantitative description of a model system, we show that a second gene copy serves to reduce gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. (elifesciences.org)
  • Identifying the genes that confer these conditionally beneficial effects to particular chromosomal duplications can improve our understanding of the genetic and molecular mechanisms that enable certain aneuploidies to persist in cell populations and contribute to disease and evolution. (g3journal.org)
  • Molecular genetic analysis of the BRI gene in the Danish kindred showed a different defect, namely the presence of a 10-nt duplication (795-796insTTTAATTTGT) between codons 265 and 266, one codon before the normal stop codon 267. (antibody-antibodies.com)
  • The result was often the formation of families of hundreds of related genes that now can be recognized by amino acid sequence similarity as well as functional similarity. (pnas.org)
  • Functional divergence between the duplicate genes is another possible fate. (wikipedia.org)
  • Gene duplication and subsequent functional divergence of duplicate genes is one of the most important mechanisms for the evolution of novel gene function ( 1 - 5 ). (pnas.org)
  • In the latter case the rate of nonsynonymous nucleotide substitution may also be enhanced because of relaxation of functional constraints of redundant genes after gene duplication ( 8 ), but the rate will never exceed that of synonymous substitution. (pnas.org)
  • Functional diversification of lepidopteran opsins following gene duplication. (biomedsearch.com)
  • Alternatively, a chimeric gene may also be pathogenic by different gain-of-function mechanisms that are not restricted to dose-sensitive genes: the emergence of a new polypeptide that combines functional domains from two different genes, the deregulated expression of any coding sequence by the promoter region of a neighboring gene, and/or a putative dominant-negative effect due to the preservation of functional domains of partially truncated proteins. (hindawi.com)
  • The new fusion protein might be pathogenic due to different mechanisms: the emergence of a new polypeptide that combines functional domains from two different genes, the deregulated expression of any coding sequence by the promoter region of a neighboring gene and/or a putative dominant-negative effect due to the preservation of functional domains of partially truncated proteins. (hindawi.com)
  • During vertebrate evolution, duplicated hemoglobin (Hb) genes diverged with respect to functional properties as well as the developmental timing of expression. (unl.edu)
  • The main goal of this study was to conduct a functional analysis of the three AP3 orthologs present in Thalictrum thalictroides , representing the paleo AP3 gene lineage, to determine the degree of redundancy versus divergence after gene duplication. (frontiersin.org)
  • To address these questions, we undertook functional characterization by virus-induced gene silencing (VIGS), protein-protein interaction and binding site analyses. (frontiersin.org)
  • The functional significance and global prevalence of this duplication, and whether there are other copy number variations at the PvDBP locus, is unknown. (harvard.edu)
  • It is therefore unlikely that PvDBP duplication is associated with infection of DARC-negative individuals, but functional tests will be required to confirm this hypothesis. (harvard.edu)
  • It remains unclear to what extent multiple copies of clock gene family members are functionally redundant or have allowed for functional diversification. (prolekare.cz)
  • By comparing expression patterns across multiple tissues, and during development, we present evidence for gene- and tissue-specific divergence in expression patterns, consistent with functional diversification of clock gene duplicates. (prolekare.cz)
  • Clock Gene Evolution and Functional Divergence. (prolekare.cz)
  • Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. (ugent.be)
  • By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication. (ugent.be)
  • On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. (uni-muenchen.de)
  • Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. (biomedcentral.com)
  • The HSP and HSF paralogs apparently arose from gene duplications and subsequent diversification. (plantphysiol.org)
  • These 'extra' genes are, in principle, available for the evolution of new functions that could drive the origin of novelties and thus contribute to the diversification of life on Earth. (anr.fr)
  • For instance, it has been shown that the diversification of gene families involved in cell differentiation and cell-cell communication contributed to the origination of multicellularity [ 1 ]. (biomedcentral.com)
  • Polyploidy, or whole genome duplication is a product of nondisjunction during meiosis which results in additional copies of the entire genome. (wikipedia.org)
  • Further, if we may consider one copy (the effective gene) as being conserved relatively unchanged as a result of selection pressure, so that the function it specifies is neither lost nor adversely modified, other copies would be free to mutate as long as deleterious gene products did not result. (pnas.org)
  • These copies would initially have the capacity to specify a complete gene product-for example, an enzyme or part of a physiological system. (pnas.org)
  • There has been the formation of gene copies that then may evolve for a time free of selection and take on new or variant functions. (pnas.org)
  • Evolution by gene duplication is an event by which a gene or part of a gene can have two identical copies that can not be distinguished from each other. (wikipedia.org)
  • The more copies of the same (duplicated) gene a cell has in its genome, the more gene product can be produced simultaneously. (wikipedia.org)
  • Gene duplication is a process where a DNA region coding for a gene duplicates, making additional copies of itself within the same genome. (jove.com)
  • These duplicated copies of the gene - called paralogs can later mutate and diverge in one of the following ways. (jove.com)
  • The duplicated copies of the gene are called Paralogs. (jove.com)
  • However, specific examples of how genes change to maintain two paralogous gene copies within an organism are relatively rare. (sciencemag.org)
  • It is important to highlight that our models sidestep the issue of hidden paralogy by ``integrating out" the possible orthology assignments of gene copies. (rice.edu)
  • Sometimes the copies are flawed and the genes contained within them are mutated - the process that drives evolution. (ace-net.ca)
  • Sometimes extra copies of genes are produced. (ace-net.ca)
  • When two copies of a gene are both functioning within a genome they can take on different roles," says Clark. (ace-net.ca)
  • Healthy cells in humans possess two copies of each gene. (medizin-aspekte.de)
  • For their experiments, the researchers mutated one of the two copies of the KRAS gene in mice. (medizin-aspekte.de)
  • It therefore appears that the cell amplifies the growth signal due to the presence of extra gene copies. (medizin-aspekte.de)
  • All of the isolates with duplicated copies had 1 allelic family for each of the 3 genes ( msp1 , msp2 , and glurp ), confirming that these infections were single and not mixed. (cdc.gov)
  • ddPCR assays with locked nucleic acid (LNA) TaqMan probes revealed that transgenic Ndn expression was almost equal to endogenous Ndn expression, despite there being two copies of the Ndn gene in the transgene, indicating an interaction between the transcriptional regulation of endogenous Ndn and the transgene. (springer.com)
  • Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. (biomedcentral.com)
  • We conclude that the hemolytic phenotype of VIB 645 is not due to increased expression of one or both copies of the vhh gene. (stir.ac.uk)
  • duplication resulted in five ancestral copies in land plants, forming five fundamental monophyletic groups in the phylogenetic tree. (springer.com)
  • We're equating redundancy-having multiple copies of the same gene present in the genome-to rapid change. (umich.edu)
  • It is unclear whether extra copies of these other genes affect the severity of the condition. (medlineplus.gov)
  • In females (who have two X chromosomes), a duplication of one of the two copies of the gene typically does not cause the disorder, but can be associated with behavioral and psychiatric symptoms such as depression , anxiety, and features of autism spectrum disorder that affect communication and social interaction. (medlineplus.gov)
  • This means instead of two copies of the genes in this segment, each cell of the body now has three copies. (globalgenes.org)
  • Using inferred nucleotide sequences of ancestral organisms, we showed that the rate of nonsynonymous nucleotide substitution was significantly higher than that of synonymous substitution for the ECP gene. (pnas.org)
  • Phylogenetic analysis of DNA sequences ( 19 ) has suggested that the ECP and EDN genes were produced by tandem gene duplication from an EDN-like ancestral gene after divergence of OW and NW monkeys but before separation of hominoids and OW monkeys (see Fig. 1 ). (pnas.org)
  • Guyot, Keller: Ancestral genome duplication in rice. (springer.com)
  • The partitioning of ancestral functions in a fungal transcription factor appeared to be affected by competitive interference between the newly formed gene duplicates. (sciencemag.org)
  • Most models of gene duplication assume that the ancestral functions of the preduplication gene are independent and can therefore be neatly partitioned between descendant paralogs. (sciencemag.org)
  • duplication of an ancestral sequence. (deepdyve.com)
  • The salmonid transcriptome reveals a complex history of gene duplication that is consistent with an ancestral salmonid genome duplication hypothesis. (biomedcentral.com)
  • Genes that make up families are hypothesized to have arisen from a common ancestral sequence through gene duplication, which adds an extra copy of a gene to the organism's genome. (umich.edu)
  • The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. (biomedcentral.com)
  • Polyploidy is common in plants, but it has also occurred in animals, with two rounds of whole genome duplication (2R event) in the vertebrate lineage leading to humans. (wikipedia.org)
  • For instance, whole genome duplications are postulated to have had a major impact on the vertebrate lineage ( O hno 1970 , 1998 ). (genetics.org)
  • A second duplication at the time of the gnathostomes took place in the lobbed-fin fish lineage leading to mammals, so at 420 Myr ago. (mad-cow.org)
  • The conservation between the multiple forms of gallin in the chicken genome compared with the conservation between gallin and other avian gallin like peptides, suggests that the gene duplication has occurred relatively recently in the chicken lineage. (archives-ouvertes.fr)
  • We addressed this problem through an analysis of clock gene expression in the Atlantic salmon, a representative of the salmonids, a group which has undergone at least 4 rounds of WGD since the base of the vertebrate lineage, giving an unusually large complement of clock genes. (prolekare.cz)
  • A large degree of recent and lineage-specific gene duplications were found, that were mainly enriched in functions related to genome transposition, immune response and response to stimulus. (csic.es)
  • Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split of plants and animals/fungi is not clear. (biomedcentral.com)
  • Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. (pnas.org)
  • During the course of evolution, the globin gene duplicated and sub functionalized into two slightly different genes coding for α- and β-globin proteins, that associate to form the hemoglobin molecule with 4 subunits found in most present day vertebrates. (jove.com)
  • However, soon after birth, the β-globin gene takes over production of the β-globin proteins. (jove.com)
  • here, we show that a natural consequence of duplication and divergence of such proteins can be competitive interference between the paralogs. (sciencemag.org)
  • Because many proteins form cooperative assemblies, resolution of paralog interference is likely to be a widespread phenomenon influencing the fate of duplicated genes. (sciencemag.org)
  • The fact that many extant proteins contain duplicated domains suggests that present-day complex proteins have evolved from simple proteins mainly via domain duplication. (psu.edu)
  • Genes for essential proteins are not subject to mutational change d. (coursehero.com)
  • A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). (pnas.org)
  • The development of a gene specifying a new function from remaining elements of an older gene that had been protected from adverse selection pressure by copying seems to be far more probable than its development de novo from a random nucleotide sequence. (pnas.org)
  • It appears that none attempt to estimate the percentage of human genes that have been derived by duplication by means of studies of sequence similarity at open criterion. (pnas.org)
  • There is little doubt that duplication or copying of genes has been an ancient process, and as a result of the long time span, the earliest sequence similarities have been lost because of amino acid sequence drift. (pnas.org)
  • The purpose of this work has been to count the number of still recognizable sequence similarities and estimate the fraction of the present human genes that may have resulted from duplication. (pnas.org)
  • Remnants of the whole genome duplication of Saccharomyces cerevisiae are apparent in its genome sequence ( W olfe and S hields 1997 ). (genetics.org)
  • DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution. (jove.com)
  • The 5′ untranslated region (UTR) and part of the promoter sequence of the gene derives from AnnX , whereas the translated part and all 300 base pairs (bp) of the 3′ UTR come from the Cdic gene. (evolutionnews.org)
  • The sequence analysis of the abnormal PCR products revealed that 23 of 24 showed internal tandem duplication with or without insertion of nucleotides. (nature.com)
  • Duplication takes place in the sequence coding for the JM domain and leaves the TK domain intact. (nature.com)
  • However, no disease-related mutation that altered the DNA sequence of this gene was found. (healthcanal.com)
  • Clark says that now that technology to sequence genes has gotten much cheaper and faster, there has been an explosion of new genetic knowledge and ideas recently. (ace-net.ca)
  • The duplication/insertion leads to an altered amino acid sequence starting at codon 84 (T→L). After leucine, an additional 25 amino acids, MARKCSV-PLVMAWLTWTTSRAPLPH, followed by a stop codon at nt 511 to 513, are coded for by the mutant sequence. (haematologica.org)
  • Sequence comparison aiming to elucidate the origin of the unique features of CYP4A21 revealed a region of decreased sequence identity from exon 6 to exon 8, strongly suggesting that gene conversion could have contributed to the evolution of CYP4A21 . (biochemj.org)
  • Sequence analysis of the HOXA13 gene showed a heterozygous 18 bp duplication in the second polyalanine tract, resulting in six additional alanines. (bmj.com)
  • We find high sequence variability, both within and between populations, and expanded copy number for long-wave sensitive (LWS) opsin genes. (uzh.ch)
  • Sequence analysis characterized it as an intragenic tandem duplication leading to a frame shift with a premature stop codon in EHMT1 . (biomedcentral.com)
  • N-terminal sequence analysis of isolated leptomeningeal amyloid fibrils revealed homology to ABri, the peptide originated by a point mutation at the stop codon of gene BRI in familial British dementia. (antibody-antibodies.com)
  • The decamer duplication mutation produces a frame-shift in the BRI sequence generating a larger-than-normal precursor protein, of which the amyloid subunit (designated ADan) comprises the last 34 C-terminal amino acids. (antibody-antibodies.com)
  • For instance, the neofunctionalization model posits that soon after duplication, one of the duplicates evolves a new function that can be selected for and, thereby, maintained over time ( 2 , 3 ). (sciencemag.org)
  • Two of these fragments were tandem tail-to-tail duplicates of 77 kb and 37 kb that both contained a Ndn gene. (springer.com)
  • Loehlin DW, Carroll SB (2016) Expression of tandem gene duplicates is often greater than twofold. (springer.com)
  • The population genetic mechanisms governing the preservation of gene duplicates, especially in the critical very initial phase, have remained largely unknown. (elifesciences.org)
  • Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication. (elifesciences.org)
  • Duplicates that have been created by large-scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. (ugent.be)
  • The system utilized the antibiotic resistance properties of the gene to test factors involved in maintenance and divergence of duplicates. (utexas.edu)
  • However, linking the adaptation and duplication of HS genes is difficult because a loss of function of one of the duplicates may not lead to an alteration in phenotype such as thermotolerance, which was often attributed to gene redundancy. (plantphysiol.org)
  • After gene duplication, one of the duplicates might be released from selective pressure and have the potential to evolve new functions ('neofunctionalization') [ 4 ]. (biomedcentral.com)
  • Three lines of evidence suggest that these duplicated blocks of genes arose from a whole genome duplication event rather than by successive segmental duplications ( W olfe and S hields 1997 ). (genetics.org)
  • First, most of the duplicated blocks have the same orientation with respect to the telomere, a situation that would not be expected for segmental duplications. (genetics.org)
  • Second, if the duplications are due to successive segmental duplications, several triplicated blocks would be expected to have occurred on the basis of Poisson probability, but none are found. (genetics.org)
  • Using nucleotide substitution rate estimates for exons and introns, we show that two large segmental duplications, of six and seven human PRAME genes respectively, occurred in the last 3 million years. (biomedcentral.com)
  • During this process, tandem duplications had only a small contribution, whereas polyploidy events and large-scale segmental duplications appear to be the main driving force. (springer.com)
  • Evolution by gene duplication is a form of exaptation. (creation.com)
  • Although first discussed by Haldane in 1932 and Miller in 1935, it was not discussed in detail until 1970 in Susumu Ohno's book, Evolution by Gene Duplication . (creation.com)
  • 5. Ohno S. Evolution by Gene Duplication. (prolekare.cz)
  • Furthermore, rapid evolution of protein phosphorylation motifs, usually embedded within rapidly evolving intrinsically disordered regions is another contributing factor for survival and rapid adaptation/neofunctionalization of duplicate genes. (wikipedia.org)
  • Finally, an alternative interpretation for the short half-life of duplicate genes before silencing may deserve consideration. (sciencemag.org)
  • They estimated a mean half-life of 4 million years, concluding that "the fate awaiting most gene duplications appears to be silencing rather than preservation," and, hence, that "duplicate genes may only rarely evolve new functions. (sciencemag.org)
  • We propose that paralog interference is a common constraint on gene duplicate evolution, and its resolution, which can generate additional regulatory complexity, is needed to stabilize duplicated genes in the genome. (sciencemag.org)
  • Duplicate genes are maintained by purifying selection or evolve novel function. (utexas.edu)
  • Two recent opsin gene duplication events were found within the papilionid but not within the nymphalid butterfly families through neighbor-joining, maximum parsimony, and maximum likelihood phylogenetic analyses of 13 lepidopteran opsin sequences. (biomedsearch.com)
  • A detailed consideration of the results for one C. elegans transcription factor gene family, the Six family, comprising ceh-32, ceh-33, ceh-34 and unc-39 illustrates the value of these analyses. (harvard.edu)
  • Transcriptional analyses across six different tissues (anterior and posterior intestine, skeletal muscle, liver, gills, spleen) indicated that gene duplication preferentially affected genes expressed in two or more tissues. (csic.es)
  • Genome analyses have revealed that gene duplication in plants is rampant. (ugent.be)
  • Extensive phylogenetic analyses of the gene families show that, among nearly 2,600 orthogroups identified, at least 300 of them still retain duplication that occurred before the divergence of the three kingdoms. (biomedcentral.com)
  • Our phylogenetic analyses show that numerous gene duplications happened at the early stage of eukaryotic evolution, probably before the separation of known major eukaryotic lineages. (biomedcentral.com)
  • Since a gene duplication occurs in only one cell, either in a single-celled organism or in the germ cell of a multi-cellular organism, its carrier (i.e. the organism) usually has to compete against other organisms that do not carry the duplication. (wikipedia.org)
  • 1 How life evolved from a few primordial genes to the tens of thousands of genes in higher organisms is still a major issue in Darwinism. (creation.com)
  • 2-6 Shanks concluded that 'duplication is the way in which organisms acquire new genes. (creation.com)
  • Processes occurring in various organisms by which new genes are copied. (jove.com)
  • Gene duplication and divergence increased the capacity of organisms to adapt to environmental change ( Conant and Wolfe, 2008 ). (plantphysiol.org)
  • In addition, the continuous gene duplication pattern displayed by the cone snails has not been observed in other organisms, according to U-M researchers Dan Chang and Thomas Duda. (umich.edu)
  • The origin of novel gene function through gene duplication, mutation and natural selection represents one of the mechanisms by which organisms diversify and one of the possible paths leading to adaption. (umich.edu)
  • Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana . (springer.com)
  • Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. (nih.gov)
  • Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA-generating loci possess the hallmarks of inverted duplication events that formed the arms on each side of their respective foldback precursors. (nih.gov)
  • Genetic studies on flower development in the model plants Arabidopsis and Antirrhinum have yielded the 'ABC model', which predicts that the four types of floral organs (sepals, petals, stamens and carpels) are specified by the products of four gene classes, A, B, C, and the subsequently added E class, that act in combination. (washington.edu)
  • Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. (ugent.be)
  • In both Arabidopsis and tomato ( Solanum lycopersicum ), Mge1 is induced by ultraviolet B light and Mge2 is induced by heat, which suggests regulatory divergence of the genes. (plantphysiol.org)
  • Therefore, with duplication and subfunctionalization, one copy of the Arabidopsis Mge genes became specialized in a distinct type of HS. (plantphysiol.org)
  • Costaglioli P, Joubes J, Garcia C, Stef M, Arveiler B, Lessire R, Garbay B (2005) Profiling candidate genes involved in wax biosynthesis in Arabidopsis thaliana by microarray analysis. (springer.com)
  • This tandem gene duplication was also found in Y. pestis , Y. pseudotuberculosis , and Y. ruckeri but not in other bacteria. (asm.org)
  • Gene clustering and gene trees support the idea that these genes are derived from an ancient tandem gene duplication that likely predates the radiation of the seed plants and then expanded by subsequent polyploidy events. (plantcell.org)
  • Afoufa-Bastien D, Medici A, Jeauffre J, Coutos-Thevenot P, Lemoine R, Atanassova R, Laloi M (2010) The Vitis vinifera sugar transporter gene family: phylogenetic overview and macroarray expression profiling. (springer.com)
  • The additional tRNA gene findings were verified using phylogenetic analysis and genetic distance analysis. (medworm.com)
  • Here we report a biochemical, genetic, and phylogenetic comparison of metazoan Ctr 1 and Ctr 2 , suggesting that Ctr 2 arose over 550 million years ago as a result of a gene duplication event followed by loss of Cu_ transport activity. (unl.edu)
  • Here, we have studied gene duplications in early eukaryotes by phylogenetic relative dating. (biomedcentral.com)
  • Completely sequenced plastomes provide a valuable source of information about the duplication, loss, and transfer events of chloroplast genes and phylogenetic data for resolving relationships among major groups of plants. (semanticscholar.org)
  • Once a gene has been duplicated, the risk of deleterious mutation is decreased. (pnas.org)
  • The duplication in the CHM gene observed in this study represents another mechanism of mutation in the CHM gene. (arvojournals.org)
  • Based on our results, we would conservatively estimate that copy number variants in the CHM gene are likely to be found in no more that 10 per cent of cases in which no mutation is found by sequencing. (arvojournals.org)
  • Thirty-three Menkes patients in whom no mutation had been detected with standard diagnostic tools were screened for exon duplications in the ATP7A gene. (biomedcentral.com)
  • Duplications in the ATP7A gene are estimated from our material to be the disease causing mutation in 4% of the Menkes disease patients. (biomedcentral.com)
  • Traditional mutation-screening with PCR amplification of the coding region of ATP7A (23 exons) followed by sequencing, fails to detect exon duplications. (biomedcentral.com)
  • The wild-type penA gene confers clinically significant ceftazidime resistance only when overexpressed due to a promoter mutation, transcriptional anti-termination or by gene duplication and amplification (GDA). (tropmedres.ac)
  • Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. (wikipedia.org)
  • Repetitive genetic elements such as transposable elements offer one source of repetitive DNA that can facilitate recombination, and they are often found at duplication breakpoints in plants and mammals. (wikipedia.org)
  • Replication slippage is an error in DNA replication that can produce duplications of short genetic sequences. (wikipedia.org)
  • These long and continuous reads allowed the annotation of a large number of coding genes (55,423), non-coding RNA genes (2,991) and 345 Mb of mobile genetic elements. (csic.es)
  • These duplication and gene family expansions could be related in part to the activity of mobile genetic elements. (csic.es)
  • Genetic analysis revealed a 23.4-kb tandem duplication of the proximal portion of the F8 gene (promoter, exon 1 and a large part of intron 1), which co-segregated with high FVIII levels in the family and was absent in 103 normal controls. (onmedica.com)
  • Although chromosomal duplications are often deleterious, in some cases they enhance cells' abilities to tolerate specific genetic or environmental challenges. (g3journal.org)
  • Many studies focus on identification of genetic patterns and genes related to normal functions and disease. (mindzilla.com)
  • MECP2 duplication syndrome is caused by a genetic change in which there is an extra copy of the MECP2 gene in each cell. (medlineplus.gov)
  • Since these neurons had the same genetic background and had received identical sham-treatment, the researchers expected to see no correlation between gene length and changes in gene expression. (texaschildrens.org)
  • This suggested that some of the original observations about the effects of long gene could be attributed to normal genetic variation in the population and needed to be reevaluated. (texaschildrens.org)
  • Talk with a genetic counselor or specialist if you or someone in your family has been diagnosed with a 2p duplication. (globalgenes.org)
  • These findings must contribute to our comprehensive understanding of visual capabilities of zebrafish and the evolution of the fish visual system and should become a basis of further studies on expression and developmental regulation of the opsin genes. (genetics.org)
  • The floral organ identity genes are thus a logical focus to gain insight into the angiosperm radiation, since alterations to both the structure and regulation of developmental genes are known to underlie morphological diversity. (washington.edu)
  • For example, the subfamilies of genes that encode the different subunit chains of Hb are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different developmental stages. (unl.edu)
  • The differences in expression patterns of these genes at different developmental stages further support that these genes may have distinct functions. (k-state.edu)
  • Symptoms of 2p duplications may include developmental delays, intellectual difficulties, communication difficulties, difficulties with gross and fine motor skills, and heart and breathing (respiratory) issues. (globalgenes.org)
  • Red lines connect orthologous gene pairs between S. cerevisiae and S. castellii . (nih.gov)
  • The original gene, however, will also evolve, and such direct descendants of the original gene are called orthologous genes. (creation.com)
  • These observations have led to the suggestion that the ECP gene has been subject to positive Darwinian selection ( 19 ), but comparison of the ECP and EDN gene sequences does not show a rate of nonsynonymous substitution significantly higher than that of synonymous substitution. (pnas.org)
  • Paralogs with similar sequences and functions form a gene family. (jove.com)
  • Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. (nih.gov)
  • The sequences of the 5´-flanking regions and adjacent nucleotides in exon 1 of the CYP4A21 and CYP4A24 genes have been deposited in the EMBL database under accession numbers AJ586859 and AJ586860 , respectively. (biochemj.org)
  • A. Drift has modified the base sequences in some AFCP genes. (coursehero.com)
  • We describe a patient originating from Ghana who had combined heterozygous -α 4.2 thalassemia, ααα anti3.7 triplication, the common δ globin variant HbA 2 ' and a new 65 bp duplication/insertion in exon II of the β globin gene causing β 0 -thalassemia. (haematologica.org)
  • A duplication of a 65 bp long piece of exon II from nt 367 to nt 431 was demonstrated. (haematologica.org)
  • The shaded area represents the wild-type part of exon II, the clear area shows the 65 bp duplication. (haematologica.org)
  • The ATP7A gene was screened for exon duplications using multiplex ligation-dependent probe amplification (MLPA). (biomedcentral.com)
  • In the OHS patient with a duplication of exon 3 and 4, the duplicated out-of-frame transcript coexists with an almost equally represented wild-type transcript, presumably leading to the milder phenotype. (biomedcentral.com)
  • This study provides insight into exon duplications in the ATP7A gene. (biomedcentral.com)
  • Duplications arise from an event termed unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes. (wikipedia.org)
  • The duplication was not seen in 200 ethnically matched normal chromosomes. (molvis.org)
  • As a result, Y chromosomes are unable to respond efficiently to selection, and newly formed Y chromosomes degenerate until few genes remain. (cam.ac.uk)
  • The rapid loss of genes from newly formed Y chromosomes has been well studied, but gene loss from highly degenerate Y chromosomes has only recently received attention. (cam.ac.uk)
  • Only a small amount of paralogous gene loss (4-6%) occurred after speciation. (nih.gov)
  • S. cerevisiae genes are depicted in blue with blue lines connecting paralogous gene pairs. (nih.gov)
  • Such a new gene is called a paralogous gene. (creation.com)
  • Interestingly, genes involved in regulation are preferentially retained. (wikipedia.org)
  • Internal tandem duplication of the FLT3 gene is preferentially seen in acute myeloid leukemia and myelodysplastic syndrome among various hematological malignancies. (nature.com)
  • A recent study from the laboratory of Dr. Zhandong Liu , associate professor at Baylor College of Medicine and investigator at the Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital shows that expression of long genes is not preferentially altered in MeCP2 syndromes. (texaschildrens.org)
  • Assuming that no regulatory feedback loops exist that automatically down-regulate gene expression, the amount of gene product (or gene dosage) will increase with each additional gene copy, until some upper limit is reached or sufficient gene product is available. (wikipedia.org)
  • The quantitative RT-PCR revealed a considerable difference among the opsin genes in the expression level in the retina. (genetics.org)
  • The expression of the two red opsin genes and of three green opsin genes, RH2-1, RH2-3 , and RH2-4 , is significantly lower than that of RH2-2, SWS1 , and SWS2 . (genetics.org)
  • All the genes forming the fusion transcript might have an important role in the central nervous system (CNS) development and/or in gene expression regulation and therefore may contribute to the phenotype of both patients. (hindawi.com)
  • These changes often alter the expression of the affected gene in ways that lead to cancer and other diseases. (healthcanal.com)
  • The high proportion of Promoterome reporter fusions that drove GFP expression, compared to previous studies, led to the hypothesis that transcription factor genes might be involved in local gene duplication events less frequently than other genes. (harvard.edu)
  • Conclusions: The relatively recent evolution of multiple forms of a member of a new defensin related group of peptides that we have termed ovodefensins, may be an adaptation to increase expression or the first steps in divergent evolution of the gene in chickens. (archives-ouvertes.fr)
  • Across taxa, circadian control of physiology and behavior arises from cell-autonomous oscillations in gene expression, governed by a networks of so-called 'clock genes', collectively forming transcription-translation feedback loops. (prolekare.cz)
  • In contrast to mammals, we found no evidence for coupling between cortisol and circadian gene expression, but cortisol mediated non-circadian regulated expression of a subset of clock genes in the salmon gill was evident. (prolekare.cz)
  • Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence. (ugent.be)
  • In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in. (ugent.be)
  • By heterologous expression in Escherichia and the correlation of gene expression patterns to the glucosinolate phenotype, we show that AOP2 catalyzes the conversion of methylsulfinylalkyl glucosinolates to alkenyl glucosinolates. (plantcell.org)
  • and this dispersion contributes to divergent gene expression and morphological novelties. (plantcell.org)
  • The gene models were confirmed by cloning and sequencing of the corresponding cDNAs and gene expression profiles during insect development were determined. (k-state.edu)
  • Of these, the expression of OsHMP37 was far higher than that of the other seven genes while OsHMP28 was expressed exclusively in the roots. (frontiersin.org)
  • Many neurodevelopmental disorders are caused by misregulation of master regulatory genes that control the expression and activity of thousands of downstream target genes. (texaschildrens.org)
  • Preferential dysregulation of long genes in neurodevelopmental disorders such as autism, Rett syndrome, Fragile X syndrome, Angelman syndrome has been a recurring theme in many large-scale gene expression studies. (texaschildrens.org)
  • Ayush Raman , a graduate student in the Liu lab and the first author of this study, scrambled gene expression data obtained from cortical neurons of mice. (texaschildrens.org)
  • The data was divided into 'control' and 'experimental' groups and the researchers looked for correlations between gene length and changes in gene expression patterns. (texaschildrens.org)
  • As expected, topotecan treatment caused a stronger downregulation of long genes, indicating that this statistical correction is able to pick out strong and likely, authentic changes in gene expression. (texaschildrens.org)
  • Next, using this background variation ('noise') as the baseline, they analyzed the gene expression changes in 15 publicly available datasets of MeCP2 studies across 28 different tissue types. (texaschildrens.org)
  • Recent studies yielded a first direct estimate of the genome-wide rate of gene duplication in C. elegans, the first multicellular eukaryote for which such as estimate became available. (wikipedia.org)
  • New World (NW) monkeys have only one gene that is homologous to the ECP and EDN genes of hominoids and OW monkeys ( 19 ). (pnas.org)
  • What are homologous genes? (brainscape.com)
  • Mre11 inactivation appears not to affect VSG gene switching during antigenic variation of a laboratory strain, which is perhaps surprising given the importance of homologous recombination during this process. (lancs.ac.uk)
  • Several models exist that try to explain how new cellular functions of genes and their encoded protein products evolve through the mechanism of duplication and divergence. (wikipedia.org)
  • The so-called 'dosage' of a gene refers to the amount of mRNA transcripts and subsequently translated protein molecules produced from a gene per time and per cell. (wikipedia.org)
  • The genes for eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) in primates belong to the ribonuclease gene family, and the ECP gene, whose product has an anti-pathogen function not displayed by EDN, was generated by duplication of the EDN gene about 31 million years ago. (pnas.org)
  • In this paper we present a convincing case of positive selection that occurred during the early stage of divergence of the duplicated eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) genes in primates. (pnas.org)
  • genes (in purple) are labeled according to their top S. cerevisiae match by a BLASTX comparison to S. cerevisiae protein-coding genes. (nih.gov)
  • However, the protein products of the two paralogous genes complement each other and exhibit the original gene function. (jove.com)
  • Gene duplication is one of the major drivers of the evolution of gene and protein networks. (sciencemag.org)
  • An elevated rate of evolution was detected in the red-shifted Papilio Rh3 branch following gene duplication, because of an increase in the amino acid substitution rate in the transmembrane domain of the protein, a region that forms the chromophore-binding pocket of the visual pigment. (biomedsearch.com)
  • The evidence for promiscuous protein-protein interactions via yeast two-hybrid combined with the detection of AP3 specific binding motifs in all B-class gene promoters provide partial support for these hypotheses. (frontiersin.org)
  • Inverse PCR was used to amplify major cold shock protein (MCSP) gene families from a diverse range of bacteria, including the psychrotolerant Yersinia enterocolitica , which was found to have two almost identical MCSP coding regions ( cspA1 and cspA2 ) located approximately 300 bp apart. (asm.org)
  • Here we show that the Saccharomyces cerevisiae MPS1 gene product, an essential protein kinase required for spindle pole body (SPB) duplication (Winey et al. (rupress.org)
  • We propose that the essential MPS1 protein kinase functions both in SPB duplication and in a mitotic checkpoint monitoring spindle integrity. (rupress.org)
  • Recall the Antarctic fishes that have an AFCP gene that produces an antifreeze protein? (coursehero.com)
  • The MECP2 gene provides instructions for making a protein called MeCP2 that is critical for normal brain function. (medlineplus.gov)
  • Researchers believe that this protein has several functions, including regulating other genes in the brain by controlling when they are able to participate in protein production. (medlineplus.gov)
  • An extra copy of the MECP2 gene leads to the production of excess MeCP2 protein and an increase in protein function. (medlineplus.gov)
  • 2 ) reported 9- to 15-fold differences in S values and a flat distribution of S for 24 single-copy genes in Drosophila . (sciencemag.org)
  • Here, we show that Alms1a, a Drosophila homolog of the human ciliopathy gene Alstrom syndrome, is enriched on the mother centrosome in Drosophila male germline stem cells (GSCs). (elifesciences.org)
  • These data strengthen the conclusion that male reproductive genes may often be under directional selection in Drosophila. (utexas.edu)
  • Much before the evolution of modern apes, the early primates had dichromatic vision due to the presence of the Blue and Green opsin genes. (jove.com)
  • 200 publications in the last 10 years ( www.nslij-genetics.org/duplication ). (pnas.org)
  • Even though, it is still stunningly unclear to what extent natural selection could also take part in the process that drives the fixation, and also initial maintenance, of duplicated genes according to population genetics ( Lynch, 2007 ). (elifesciences.org)
  • On the other hand, S. castellii appears to have lost several hundred genes that were not retained as duplicated paralogs. (nih.gov)
  • Although in some instances this competition may be advantageous, we suspect that paralog interference following gene duplication would typically have detrimental effects that must be evolutionarily bypassed for the paralogs to be maintained. (sciencemag.org)
  • Taken together, these studies illustrate the different fates that floral organ identity gene paralogs can assume following duplication that can ultimately be relevant to the generation of biodiversity. (washington.edu)
  • 1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. (biomedcentral.com)
  • However, it was argued that, as natural selection does not 'know' which duplicated gene should be under selection and which is free of selective constraint, both paralogs experience a period of relaxed selection and accelerated evolution. (biomedcentral.com)
  • Gene duplication can arise due to the following four reasons. (jove.com)
  • We're interested in how the the duplicated genes function and also in the mechanism that causes the duplications to arise. (ace-net.ca)
  • These multigene families are subject to birth-and-death evolution and most new genes arise by gene duplication [ 3 ]. (biomedcentral.com)
  • of elements from several preexisting genes. (pnas.org)
  • Although one or more whole genome duplications are believed to have influenced vertebrate evolution, polyploidy of contemporary mammals is generally incompatible with normal development and function of all but a few tissues. (creation.com)
  • Whole genome duplication plays an important role in the evolution of plants and some vertebrate groups. (utexas.edu)
  • JAK function has been implicated in hematopoiesis and regulation of the immune system, and recent data suggest that the vertebrate JAK2 gene may play a role in leukemia. (epfl.ch)
  • In marine fishes the population structure is expected to be weak because of extensive gene flow, and it might be questioned whether adaptive responses to changes in physico-chemical conditions or selective harvesting have occurred in this large vertebrate group. (biomedcentral.com)
  • After a whole genome duplication, there is a relatively short period of genome instability, extensive gene loss, elevated levels of nucleotide substitution and regulatory network rewiring. (wikipedia.org)
  • It is unclear whether the element is a translational enhancer or has some other regulatory role in the AnnX gene such as, for example, the mRNA localization. (evolutionnews.org)
  • We also identified two large gene clusters that jointly encompass many key phenotypic regulatory Type II MADS-box gene clades ( SEP1 , SQUA , TM8 , SEP3 , FLC , AGL6 , and TM3 ). (plantcell.org)
  • Our findings add to a growing body of literature that shows the conditionally beneficial effects of chromosomal duplication are typically mediated by a small number of genes that enhance tolerance to specific stresses when their copy numbers are increased. (g3journal.org)
  • We have been particularly interested in recent duplications in the human genome as examples of relatively large-scale changes to our genome. (biomedcentral.com)
  • We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities. (nih.gov)
  • The second mechanism is the use of gene duplication. (plantcell.org)
  • This mechanism is formally similar to classical transposon insertion, but the duplication is much longer, often in the range of 100bp. (semanticscholar.org)
  • The adverse effects of gene duplication, such as Down's syndrome, are well known. (creation.com)
  • 4, 10 Hypospadias is also a manifestation in some rare single gene traits affecting sex differentiation, for example, the X linked partial androgen insensitivity syndrome and the recessive 5-alpha-reductase deficiency. (bmj.com)
  • 12, 13 Larger deletions have not yet been found in boys, and duplications of MECP2 have not yet been reported as a cause for typical Rett syndrome at all. (bmj.com)
  • We have established quantitative PCR for diagnosis of deletions affecting MECP2 , and in this paper, we report a boy manifesting clinical features of Rett syndrome and a submicroscopic duplication within the cytogenetic band Xq28 encompassing the entire MECP2 gene. (bmj.com)
  • We describe a complete duplication of MECP2 due to a submicroscopic duplication of approximately 430 kb within Xq28 in a boy with severe mental retardation and features of Rett syndrome. (bmj.com)
  • Partial ATP7A gene duplication was identified in 20 unrelated patients including one patient with Occipital Horn Syndrome (OHS). (biomedcentral.com)
  • MECP2 duplication syndrome is a condition that occurs almost exclusively in males and is characterized by moderate to severe intellectual disability. (medlineplus.gov)
  • Individuals with MECP2 duplication syndrome have delayed development of motor skills such as sitting and walking. (medlineplus.gov)
  • Many individuals with MECP2 duplication syndrome have recurrent respiratory tract infections. (medlineplus.gov)
  • These neuronal changes disrupt normal brain activity, causing the signs and symptoms of MECP2 duplication syndrome. (medlineplus.gov)
  • MECP2 duplication syndrome is inherited in an X-linked pattern. (medlineplus.gov)
  • Loss of MeCP2 function results in Rett syndrome whereas its overexpression results in another neurological condition, the MeCP2 duplication syndrome. (texaschildrens.org)
  • This is the first description of an intragenic duplication of EHMT1 resulting in Kleefstra syndrome. (biomedcentral.com)
  • Our example is based on the duplication of the essential MADS-box transcriptional regulator Mcm1, which is found in all fungi and regulates a large set of genes. (sciencemag.org)
  • MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target genes, many of which are involved in multicellular development. (nih.gov)
  • Analysis of the transcriptional regulation of this MCSP gene in Y. enterocolitica , performed by using both reverse transcriptase-PCR and Northern blot assays, showed there to be two cold-inducible mRNA templates arising from this locus: a monocistronic template of approximately 450 bp ( cspA1 ) and a bicistronic template of approximately 900 bp ( cspA1/A2 ). (asm.org)
  • Primer extension experiments identified a putative transcriptional start site (+1) which is flanked by a cold-box motif and promoter elements (−10 and −35) similar to those found in Escherichia coli cold-inducible MCSP genes. (asm.org)
  • 45-fold increased reporter activity in endothelial cells, potentially mediating the F8 transcriptional enhancement observed in carriers of the duplication. (onmedica.com)
  • This 'collinear' correspondence is accompanied by a gradual decrease in the transcriptional efficiency of the genes. (epfl.ch)
  • for instance, the human genome retains numerous gene family members that arose from one or two rounds of whole genome duplication (WGD) at the origin of vertebrates. (anr.fr)
  • The current primary hypothesis is that it occurred via gene duplication. (creation.com)
  • The second hypothesis holds that a gene duplication that leads to a new function is preceded by a period of 'gene sharing', such that the original, unduplicated gene encodes two distinct functions. (biomedcentral.com)
  • 16 He concludes that for both vertebrates and invertebrates only when single genes, or a few genes, are duplicated is the possibility to evolve new genes created. (creation.com)
  • In this model, a gene encoding an enzyme is duplicated, allowing one copy to evolve a new product profile while the other copy maintains its original function ( Lynch and Force, 2000 ). (plantcell.org)
  • GENE redundancy is common. (genetics.org)
  • My aim was to elucidate the function of representatives of an early clade of duplicated floral organ identity genes, with a focus on determining the degree of redundancy vs. divergence amongst them and of conservation in relation to the later-diverging models. (washington.edu)
  • T (Brachyury) gene duplication confers major susceptibility to familial chordoma. (healthcanal.com)
  • Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. (elifesciences.org)
  • We report on three nonrelated patients with intellectual disability and CNVs that give rise to three new chimeric genes. (hindawi.com)
  • Fusion oncogenes are well known, but in other pathologies, the search for chimeric genes is disregarded. (hindawi.com)
  • This paper describes three nonrelated patients with ID and different CNVs detected by array-CGH, generating different chimeric genes confirmed by different strategies. (hindawi.com)
  • Amplification and overexpression of the Plasmodium falciparum multidrug resistance 1 gene ( Pfmdr1 ) have been associated with mefloquine resistance in P. falciparum malaria in Asia ( 1 ). (cdc.gov)
  • We designed a multiplex ligation-dependent probe amplification (MLPA) assay kit for the detection of copy number variants in the CHM gene. (arvojournals.org)
  • Amplification of the whole β globin gene from nt − 109 to + 1949 3′ UTR (all nt positions are given relative to the CAP site=nt 1) using primers Common C and B designed by Old et al . (haematologica.org)
  • Burkholderia pseudomallei acquired ceftazidime resistance due to gene duplication and amplification. (tropmedres.ac)
  • There is significant interplay between accessory helicases and recombination enzymes in both bacteria and lower eukaryotes but how these replication repair systems interact to ensure efficient genome duplication remains unclear. (mdpi.com)
  • Gene duplications play a major role in evolution by providing paralogous genes that can acquire specialized functions over time ( O hno 1970 ). (genetics.org)
  • Gene duplications have a major role in the evolution of new biological functions. (biomedcentral.com)
  • duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached. (biomedcentral.com)
  • Besides its important role in the evolution of new gene functions, gene duplication also greatly contributes to the speciation process through the divergent resolution of duplicated genes in different populations [ 7 ]. (biomedcentral.com)
  • The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. (jove.com)
  • However, it has been difficult to measure the rate at which such duplications occur. (wikipedia.org)
  • Gene duplication does occur. (creation.com)