Loading...
*  Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene...
Gene duplication has been studied extensively. However, most studies focus on one duplication mechanism at a time or take all of the duplication mechanisms as a whole and do not consider the differences between the various mechanisms. In this study we considered the relative extent to which the various mechanisms contribute to recent gene duplications in human and mouse, and we estimated the gene duplication rate occurring via different duplication mechanisms. To achieve our goals, we studied unequal crossover and retroposition simultaneously. We quantitatively confirmed that these two processes are independent and compared their respective contributions to gene duplications. These results provide the basis of our novel strategy for estimating gene duplication rates.. In our new strategy, ...
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-8-r158
*  Gene duplication - Wikipedia
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 ...
https://en.wikipedia.org/wiki/Gene_duplication
*  Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach | BMC Evolutionary...
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 ...
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-123
*  chromosome duplication - Posts
chromosome duplication - MedHelp's chromosome duplication Center for Information, Symptoms, Resources, Treatments and Tools for chromosome duplication. Find chromosome duplication information, treatments for chromosome duplication and chromosome duplication symptoms.
http://www.medhelp.org/tags/show/94456/chromosome-duplication?section=subjects
*  Evolution of YidC/Oxa1/Alb3 insertases: three independent gene duplications followed by functional specialization in bacteria,...
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. ...
https://epub.ub.uni-muenchen.de/17726/index.html
*  Gene dosage and gene duplication | Bioinformatics and Genomics @ CRG
Everyone knows that gene duplications are of paramount importance for the emergence of new genes and new gene functions. Over the past century, many formal and verbal theories have been put forth to describe the process of evolution of new functions through gene duplications.
http://opathy.eu/evolutionary_genomics/gene_dosage_and_gene_duplication
*  Mysteries of Bony Fish Genome Evolution - Healthcanal.com : Healthcanal.com
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 ...
https://www.healthcanal.com/medical-breakthroughs/68691-mysteries-of-bony-fish-genome-evolution.html
*  Whole-genome duplication in teleost fishes and its evolutionary consequences - Zurich Open Repository and Archive
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 ...
http://www.zora.uzh.ch/id/eprint/105177/
*  Полиплоид - Википедија, слободна енциклопедија
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- ...
https://sr.wikipedia.org/wiki/%D0%9F%D0%BE%D0%BB%D0%B8%D0%BF%D0%BB%D0%BE%D0%B8%D0%B4
*  Evolution and functional divergence of the anoctamin family of membrane proteins | BMC Evolutionary Biology | Full Text
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 ...
https://0-bmcevolbiol-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1471-2148-10-319
*  Chromosomal rearrangements in the 11p15 imprinted region: 17 new 11p15.5 duplications with associated phenotypes and putative...
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. ...
http://jmg.bmj.com/content/early/2017/12/09/jmedgenet-2017-104919.full
*  Zinc-induced facilitator-like family in plants:lineage-specific expansion in monocotyledons and conserved genomic and...
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 ...
http://www.lume.ufrgs.br/handle/10183/109892
*  Resolving multicopy duplications de novo using polyploid phasing
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 ...
https://digital.lib.washington.edu/researchworks/handle/1773/39168
*  ZFIN Publication: Mellgren et al., 2002
The zebrafish pigment stripe pattern is a complex tissue containing iridophores, xanthophores and multiple melanocyte types. Mutational analysis reveals that both ancient and recent gene duplications are involved in the generation or maintenance of the pattern complexity. Receptor tyrosine kinases kit and fms, products of an ancient gene duplication, are required in distinct types of melanocytes and xanthophores. Transcription factors mitfa and mitfb, results of a teleost-specific duplication, partition gene expression and function between different sets of melanocytes. Understanding the roles of these duplicated genes in zebrafish allows us to predict roles for their precursors in ancestral vertebrates ...
http://zfin.org/ZDB-PUB-020227-3
*  Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence. |...
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 ...
http://geuvadis.org/biblio/phylogenomics_of_the_oxidative_phosphorylation_in_fungi_reveals_extensive_gene_duplication_fo
*  MBD5 Gene | 2q23.1 Deletion/Duplication Disorders
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.…
https://2q23.org/mbd5-gene/
*  Highlights | ICREA
The model yeast Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced. From the initial analyses it appeared that the organism seemed to have two very different versions of many of its genes, implying an ancestral duplication of the whole genome. Since then, the scientific community has accepted the theory that yeast underwent a whole genome duplication, a phenomenon that is not isolated and can also be found in other species. For instance, we know that whole genome duplications were important in the early evolution of vertebrates and that it is a very common phenomenon in plants, especially cultivated ones. However the mechanism by which this whole genome duplication occurred remained unknown, and highly debated.. In this article Gabaldón's team shows that the appearance of duplicated genes was not caused by a simple duplication of the whole genome but rather by a ...
https://www.icrea.cat/en/highlights?page=1
*  DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
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 ...
http://www.diva-portal.org/smash/record.jsf?dswid=-9113&pid=diva2%3A234677&c=4&searchType=SIMPLE&language=en&query=&af=%5B%5D&aq=%5B%5B%7B%22personId%22%3A%22miczo266%22%7D%5D%5D&aq2=%5B%5B%5D%5D&aqe=%5B%5D&noOfRows=50&sortOrder=author_sort_asc&onlyFullText=false&sf=all
*  Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence. | IKMB
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 ...
http://www.ikmb.uni-kiel.de/publications/disease-associated-variants-pypaf1-and-nod2-result-similar-alterations-conserved
*  DiVA - Søkeresultat
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 ...
http://www.diva-portal.org/smash/resultList.jsf?dswid=-9113&af=%5B%5D&aq=%5B%5B%7B%22personId%22%3A%22miczo266%22%7D%5D%5D&aqe=%5B%5D&aq2=%5B%5B%5D%5D&language=no&query=
*  "Wrecks of Ancient Life": Genetic Variants Vetted by Natural Selection |...
Seven times in On the Origin of Species, Darwin invoked the concept that "nature does not make leaps. Over 50 years after Darwin's 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 ...
http://www.genetics.org/content/200/3/675
*  The DNA sequence and comparative analysis of human chromosome 5.
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 ...
http://www.uniprot.org/citations/15372022
*  Evolution of a symbiotic receptor through gene duplications in the legume-rhizobium mutualism - De Mita - 2013 - New...
Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. ...
http://onlinelibrary.wiley.com/doi/10.1111/nph.12549/suppinfo
*  Thomas Maher | School of Medicine
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 ...
https://www.bumc.bu.edu/busm/profile/thomas-maher/
*  Yeast owes its brewing capacity to chromosome duplication - Oneindia
Washington, May 15 (ANI): Yeast cells' ability to convert sugar to alcohol, the key process in the production of beer and wine, can be attributed to a remarkable evolutionary process- called chromosome duplication.
https://www.oneindia.com/2010/05/15/yeastowes-its-brewing-capacity-to-chromosomeduplication.html