High rate of chimeric gene origination by retroposition in plant genomes

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	High rate of chimeric gene origination by retroposition in plant genomes
	Wang W1,2; Zheng HK 2,3; Fan CZ 4; Li J 2; Shi JJ 2,5; Cai ZQ 2; Zhang GJ 1,2,6; Liu DY 2; Zhang JG 2; Vang S 7; Lu ZK 2; Wong GKS 2; Long MY4; Wang J*2,3,7; wwang@mail.kiz.ac.cn ; mlong@uchicago.edu ; wangj@genomics.org.cn
	2006
发表期刊	PLANT CELL
ISSN	1040-4651
卷号	18 期号:8 页码:1791-1802
合作性质	其它
摘要	Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species.
资助者	This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L. ; This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L. ; This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L. ; This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L.
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收录类别	SCI
语种	英语
资助者	This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L. ; This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L. ; This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L. ; This work was sponsored by the CAS-Max-Planck Society Fellowship, a Chinese Academy of Sciences key project grant (KSCX2-SW-121), a National Science Foundation of China (NSFC) award (30325016) to distin- guished young scientists, and a NSFC key grant (30430400) to W.W. Funding was from the Chinese Academy of Sciences (GJHZ0518), the Ministry of Science and Technology of China (CNG1-04-15-7A), the Na- tional Natural Science Foundation of China (90208019, 90403130, and 30221004), the China National Grid, the Danish Platform for Integra- tive Biology, Ole Rømer grants from the Danish Natural Science Re- search Council to J.W., a National Science Foundation CAREER award (MCB0238168), a National Institutes of Health R01 grant (R01GM065429- 01A1), and from the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to M.L.
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/4815
专题	基因起源组细胞与分子进化重点实验室
通讯作者	wwang@mail.kiz.ac.cn; mlong@uchicago.edu; wangj@genomics.org.cn
作者单位	1.CAS-Max-Plank Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 2.Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3.Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark 4.Department of Ecology and Evolution, University of Chicago, Chicago 60637, Illinois 5.Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan 250014, China 6.Graduate School of Chinese Academy Sciences, Beijing 100039, China 7.Institute of Human Genetics, University of Aarhus, DK-8000, Aarhus C, Denmark
推荐引用方式 GB/T 7714	Wang W*,Zheng HK,Fan CZ,et al. High rate of chimeric gene origination by retroposition in plant genomes[J]. PLANT CELL,2006,18(8):1791-1802.
APA	Wang W*.,Zheng HK.,Fan CZ.,Li J.,Shi JJ.,...&wangj@genomics.org.cn.(2006).High rate of chimeric gene origination by retroposition in plant genomes.PLANT CELL,18(8),1791-1802.
MLA	Wang W*,et al."High rate of chimeric gene origination by retroposition in plant genomes".PLANT CELL 18.8(2006):1791-1802.

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