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	Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates
	Chen, Ming1,4; Zou, Ming1,4; Fu, Beide1,4; Li, Xin2; Vibranovski, Maria D.3; Gan, Xiaoni1,4; Wang, Dengqiang1,4,5; Wang, Wen2; Long, Manyuan3; He, Shunping1
刊名	PLOS ONE
	2011-07-11
卷号	6期号:7页码:e21466
关键词	NON-LTR RETROTRANSPOSONS HUMAN GENOME PROCESSED PSEUDOGENES SEX-CHROMOSOMES GENE DROSOPHILA DNA REVEALS FISH RETROGENES
ISSN号	1932-6203
通讯作者	Chen, M (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China ; mlong@uchicago.edu ; clad@ihb.ac.cn
中文摘要	The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.
英文摘要	The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.
学科主题	Life Sciences & Biomedicine - Other Topics
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	NON-LTR RETROTRANSPOSONS ; HUMAN GENOME ; PROCESSED PSEUDOGENES ; SEX-CHROMOSOMES ; GENE ; DROSOPHILA ; DNA ; REVEALS ; FISH ; RETROGENES
收录类别	SCI
资助信息	National Natural Science Foundation of China[2007CB411601]
语种	英语
WOS记录号	WOS:000292680900006
公开日期	2011-12-22
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/16399]
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
作者单位	1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China 2.Chinese Acad Sci, Kunming Inst Zool, Kunming, Yunnan Province, Peoples R China 3.Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA 4.Chinese Acad Sci, Grad Univ, Beijing, Peoples R China 5.Chinese Acad Fisheries Sci, Yangtze River Fisheries Res Inst, Wuhan, Peoples R China
推荐引用方式 GB/T 7714	Chen, Ming,Zou, Ming,Fu, Beide,et al. Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates[J]. PLOS ONE,2011,6(7):e21466.
APA	Chen, Ming.,Zou, Ming.,Fu, Beide.,Li, Xin.,Vibranovski, Maria D..,...&He, Shunping.(2011).Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates.PLOS ONE,6(7),e21466.
MLA	Chen, Ming,et al."Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates".PLOS ONE 6.7(2011):e21466.

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