Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication

doi:10.1093/molbev/mss108

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	Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication
	Guo, Baocheng 1,2; Zou, Ming 3; Wagner, Andreas 1,2; Wagner, A (reprint author), Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland.
刊名	MOLECULAR BIOLOGY AND EVOLUTION
	2012-10-01
卷号	29 期号:10 页码:3005-3022
关键词	Indel Gene Duplication Teleost Fish-specific Genome Duplication
ISSN号	0737-4038
DOI	10.1093/molbev/mss108
文献子类	Article
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.; 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.
WOS关键词	MULTIPLE SEQUENCE ALIGNMENT ; PROTEIN-CODING GENES ; RAY-FINNED FISH ; MUTATION-RATE ; FUNCTIONAL DIVERGENCE ; SECONDARY-STRUCTURE ; MAXIMUM-LIKELIHOOD ; NUCLEOTIDE SUBSTITUTION ; SOLVENT ACCESSIBILITY ; PHYLOGENETIC ANALYSIS
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
语种	英语
WOS记录号	WOS:000309927900014
资助机构	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 ; Swiss National Science Foundation [315230-129708]; YeastX project of SystemsX.ch; University Priority Research Program in Systems Biology at the University of Zurich
公开日期	2013-01-09
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/17166]
专题	水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文
通讯作者	Wagner, A (reprint author), Univ Zurich, Inst Evolutionary Biol & Environm Studies, Zurich, Switzerland.
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
推荐引用方式 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.