Vanishing GC-Rich Isochores in Mammalian Genomes
| Autor: | Laurent Duret, Gwenael Piganeau, Dominique Mouchiroud, Nicolas Galtier, Marie Sémon |
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| Přispěvatelé: | Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS) |
| Rok vydání: | 2002 |
| Předmět: |
Primates
0106 biological sciences [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT] Gene Conversion Rodentia Biology 010603 evolutionary biology 01 natural sciences Genome Evolution Molecular 03 medical and health sciences Species Specificity Genetics Animals Humans Gene conversion Allele Gene Alleles Artiodactyla 030304 developmental biology Mammals Base Composition 0303 health sciences Models Genetic Genome Human Fixation (population genetics) Evolutionary biology Human genome Synonymous substitution Isochores GC-content Research Article |
| Zdroj: | ResearcherID Europe PubMed Central Genetics Genetics, Genetics Society of America, 2002, 162, pp.1837-1848 Genetics, 2002, 162, pp.1837-1848 |
| ISSN: | 1943-2631 0016-6731 |
| DOI: | 10.1093/genetics/162.4.1837 |
| Popis: | To understand the origin and evolution of isochores—the peculiar spatial distribution of GC content within mammalian genomes—we analyzed the synonymous substitution pattern in coding sequences from closely related species in different mammalian orders. In primate and cetartiodactyls, GC-rich genes are undergoing a large excess of GC → AT substitutions over AT → GC substitutions: GC-rich isochores are slowly disappearing from the genome of these two mammalian orders. In rodents, our analyses suggest both a decrease in GC content of GC-rich isochores and an increase in GC-poor isochores, but more data will be necessary to assess the significance of this pattern. These observations question the conclusions of previous works that assumed that base composition was at equilibrium. Analysis of allele frequency in human polymorphism data, however, confirmed that in the GC-rich parts of the genome, GC alleles have a higher probability of fixation than AT alleles. This fixation bias appears not strong enough to overcome the large excess of GC → AT mutations. Thus, whatever the evolutionary force (neutral or selective) at the origin of GC-rich isochores, this force is no longer effective in mammals. We propose a model based on the biased gene conversion hypothesis that accounts for the origin of GC-rich isochores in the ancestral amniote genome and for their decline in present-day mammals. |
| Databáze: | OpenAIRE |
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