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 ...
Abstract: The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the four Hox-bearing chromosomes (the chromosomes bearing the Hox clusters; i.e. human chromosomes 2 7 12 and 17) and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the human Hox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene ...
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, ...
Ohno postulated that gene duplication plays a major role in evolution in his classic book Evolution by Gene Duplication (1970).[1] While subsequent research has overwhelmingly confirmed the key role of gene duplication in molecular evolution, research to evaluate Ohnos model for the preservation of duplicate genes (now termed neofunctionalization) is ongoing and very active. He also discovered in 1956 that the Barr body of mammalian female nuclei was in fact a condensed X chromosome.[2] In Evolution by Gene Duplication, he also suggested that vertebrate genome is the result of one or more entire genome duplications; variations of this idea have come to be known as the 2R hypothesis (also called Ohnos hypothesis). He indicated that mammalian X chromosomes are conserved among species;[3] it has been referred to as Ohnos law. He also popularized the term junk DNA for segments of the DNA that have no known function.[4][5] In 1986, Ohno authored a paper published in Immunogenetics that explored ...
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 ...
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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.
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 ...
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 ...