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题名: Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication
作者: Guo, Baocheng1, 2; Zou, Ming3; Wagner, Andreas1, 2
通讯作者: Wagner, A (reprint author), Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland.
关键词: indel ; gene duplication ; teleost ; fish-specific genome duplication
刊名: MOLECULAR BIOLOGY AND EVOLUTION
发表日期: 2012-10-01
DOI: 10.1093/molbev/mss108
卷: 29, 期:10, 页:3005-3022
收录类别: SCI
文章类型: Article
部门归属: [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
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
资助者: Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich
类目[WOS]: Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
研究领域[WOS]: Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
摘要: 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.
英文摘要: 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.
关键词[WOS]: MULTIPLE SEQUENCE ALIGNMENT ; PROTEIN-CODING GENES ; RAY-FINNED FISH ; MUTATION-RATE ; FUNCTIONAL DIVERGENCE ; SECONDARY-STRUCTURE ; MAXIMUM-LIKELIHOOD ; NUCLEOTIDE SUBSTITUTION ; SOLVENT ACCESSIBILITY ; PHYLOGENETIC ANALYSIS
语种: 英语
WOS记录号: WOS:000309927900014
ISSN号: 0737-4038
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/17166
Appears in Collections:水生生物多样性与资源保护研究中心_期刊论文

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作者单位: 1.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:
Guo, Baocheng; Zou, Ming; Wagner, Andreas.Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication,MOLECULAR BIOLOGY AND EVOLUTION,2012,29(10):3005-3022
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