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Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication
Guo, Baocheng1,2; Zou, Ming3; Wagner, Andreas1,2; Wagner, A (reprint author), Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland.
2012-10-01
Source PublicationMOLECULAR BIOLOGY AND EVOLUTION
ISSN0737-4038
Volume29Issue:10Pages:3005-3022
AbstractInsertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in five fish (teleost) species with completely sequenced genomes. The ancestor of these species has been subject to a fish-specific genome duplication (FSGD) event that occurred approximately 350 Ma. We find that duplicate genes contain at least 25% more indels than single-copy genes. These indels accumulated preferentially in the first 40 my after the FSGD. A lack of widespread asymmetric indel accumulation indicates that both members of a duplicate gene pair typically experience relaxed selection. Strikingly, we observe a 30-80% excess of deletions over insertions that is consistent for indels of various lengths and across the five genomes. We also find that indels preferentially accumulate inside loop regions of protein secondary structure and in regions where amino acids are exposed to solvent. We show that duplicate genes with high indel density also show high DNA sequence divergence. Indel density, but not amino acid divergence, can explain a large proportion of the tertiary structure divergence between proteins encoded by duplicate genes. Our observations are consistent across all five fish species. Taken together, they suggest a general pattern of duplicate gene evolution in which indels are important driving forces of evolutionary change.; Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in five fish (teleost) species with completely sequenced genomes. The ancestor of these species has been subject to a fish-specific genome duplication (FSGD) event that occurred approximately 350 Ma. We find that duplicate genes contain at least 25% more indels than single-copy genes. These indels accumulated preferentially in the first 40 my after the FSGD. A lack of widespread asymmetric indel accumulation indicates that both members of a duplicate gene pair typically experience relaxed selection. Strikingly, we observe a 30-80% excess of deletions over insertions that is consistent for indels of various lengths and across the five genomes. We also find that indels preferentially accumulate inside loop regions of protein secondary structure and in regions where amino acids are exposed to solvent. We show that duplicate genes with high indel density also show high DNA sequence divergence. Indel density, but not amino acid divergence, can explain a large proportion of the tertiary structure divergence between proteins encoded by duplicate genes. Our observations are consistent across all five fish species. Taken together, they suggest a general pattern of duplicate gene evolution in which indels are important driving forces of evolutionary change.
SubtypeArticle
KeywordIndel Gene Duplication Teleost Fish-specific Genome Duplication
Department[Guo, Baocheng; Wagner, Andreas] Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland; [Guo, Baocheng; Wagner, Andreas] Swiss Inst Bioinformat, Lausanne, Switzerland; [Zou, Ming] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China
DOI10.1093/molbev/mss108
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationSwiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich ; Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich ; Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich ; Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS IDWOS:000309927900014
WOS KeywordMULTIPLE SEQUENCE ALIGNMENT ; PROTEIN-CODING GENES ; RAY-FINNED FISH ; MUTATION-RATE ; FUNCTIONAL DIVERGENCE ; SECONDARY-STRUCTURE ; MAXIMUM-LIKELIHOOD ; NUCLEOTIDE SUBSTITUTION ; SOLVENT ACCESSIBILITY ; PHYLOGENETIC ANALYSIS
Funding OrganizationSwiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich ; Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich ; Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich ; Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/17166
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorWagner, A (reprint author), Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland.
Affiliation1.Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland
2.Swiss Inst Bioinformat, Lausanne, Switzerland
3.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China
Recommended Citation
GB/T 7714
Guo, Baocheng,Zou, Ming,Wagner, Andreas,et al. Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication[J]. MOLECULAR BIOLOGY AND EVOLUTION,2012,29(10):3005-3022.
APA Guo, Baocheng,Zou, Ming,Wagner, Andreas,&Wagner, A .(2012).Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication.MOLECULAR BIOLOGY AND EVOLUTION,29(10),3005-3022.
MLA Guo, Baocheng,et al."Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication".MOLECULAR BIOLOGY AND EVOLUTION 29.10(2012):3005-3022.
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