Evolutionary Transients in the Rice Transcriptome
In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majorit...
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| creator | Wang, Jun Zhang, Jianguo Li, Ruiqiang Zheng, Hongkun Li, Jun Zhang, Yong Li, Heng Ni, Peixiang Li, Songgang Li, Shengting Wang, Jingqiang Liu, Dongyuan McDermott, Jason Samudrala, Ram Liu, Siqi Wang, Jian Yang, Huanming Yu, Jun Wong, Gane Ka-Shu |
| description | In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as ＂evolutionary transients＂, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots. |
| doi_str_mv | 10.1016/S1672-0229(10)60023-X |
| format | Article |
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(PNNL), Richland, WA (United States)</creatorcontrib><description>In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as ＂evolutionary transients＂, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.</description><identifier>ISSN: 1672-0229</identifier><identifier>EISSN: 2210-3244</identifier><identifier>DOI: 10.1016/S1672-0229(10)60023-X</identifier><identifier>PMID: 21382590</identifier><language>eng</language><publisher>China: Elsevier Ltd</publisher><subject>60 APPLIED LIFE SCIENCES ; ARABIDOPSIS ; Arabidopsis - genetics ; BASIC BIOLOGICAL SCIENCES ; DNA, Complementary - genetics ; DNA, Plant - genetics ; Evolution, Molecular ; evolutionary transients ; Expressed Sequence Tags ; Gene Duplication ; Gene Expression Profiling ; GENES ; Genes, Plant ; Genome, Plant ; Oryza - genetics ; Oryza sativa ; PROTEINS ; RICE ; Sequence Analysis, DNA ; TRANSIENTS ; 双子叶植物 ; 基因复制 ; 核心基因 ; 水稻基因 ; 测试案例 ; 转录组</subject><ispartof>Genomics, Proteomics & Bioinformatics, 8(4):211-228, 2010-12, Vol.8 (4), p.211-228</ispartof><rights>2010 Beijing Institute of Genomics</rights><rights>Copyright © 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.</rights><rights>Copyright © Wanfang Data Co. Ltd. All Rights Reserved.</rights><rights>2010 Beijing Institute of Genomics 2010</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5091-dae82462dc69c91508c3d811bd3c1fdb243e1ab1f63a5cf85a8d7493d0e3eb923</citedby><cites>FETCH-LOGICAL-c5091-dae82462dc69c91508c3d811bd3c1fdb243e1ab1f63a5cf85a8d7493d0e3eb923</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/86775X/86775X.jpg</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054128/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S167202291060023X$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,3537,27901,27902,53766,53768,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21382590$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1009753$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Jun</creatorcontrib><creatorcontrib>Zhang, Jianguo</creatorcontrib><creatorcontrib>Li, Ruiqiang</creatorcontrib><creatorcontrib>Zheng, Hongkun</creatorcontrib><creatorcontrib>Li, Jun</creatorcontrib><creatorcontrib>Zhang, Yong</creatorcontrib><creatorcontrib>Li, Heng</creatorcontrib><creatorcontrib>Ni, Peixiang</creatorcontrib><creatorcontrib>Li, Songgang</creatorcontrib><creatorcontrib>Li, Shengting</creatorcontrib><creatorcontrib>Wang, Jingqiang</creatorcontrib><creatorcontrib>Liu, Dongyuan</creatorcontrib><creatorcontrib>McDermott, Jason</creatorcontrib><creatorcontrib>Samudrala, Ram</creatorcontrib><creatorcontrib>Liu, Siqi</creatorcontrib><creatorcontrib>Wang, Jian</creatorcontrib><creatorcontrib>Yang, Huanming</creatorcontrib><creatorcontrib>Yu, Jun</creatorcontrib><creatorcontrib>Wong, Gane Ka-Shu</creatorcontrib><creatorcontrib>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><title>Evolutionary Transients in the Rice Transcriptome</title><title>Genomics, Proteomics & Bioinformatics, 8(4):211-228</title><addtitle>Genomics Proteomics ＆ Bioinformatics</addtitle><description>In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as ＂evolutionary transients＂, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.</description><subject>60 APPLIED LIFE SCIENCES</subject><subject>ARABIDOPSIS</subject><subject>Arabidopsis - genetics</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>DNA, Complementary - genetics</subject><subject>DNA, Plant - genetics</subject><subject>Evolution, Molecular</subject><subject>evolutionary transients</subject><subject>Expressed Sequence Tags</subject><subject>Gene Duplication</subject><subject>Gene Expression Profiling</subject><subject>GENES</subject><subject>Genes, Plant</subject><subject>Genome, Plant</subject><subject>Oryza - genetics</subject><subject>Oryza sativa</subject><subject>PROTEINS</subject><subject>RICE</subject><subject>Sequence Analysis, DNA</subject><subject>TRANSIENTS</subject><subject>双子叶植物</subject><subject>基因复制</subject><subject>核心基因</subject><subject>水稻基因</subject><subject>测试案例</subject><subject>转录组</subject><issn>1672-0229</issn><issn>2210-3244</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUtvEzEUhS0EoqHwE0ARG2Ax4OvHZGYDQlV5SJWQoEjdWR77TuIwsVN7kib59Xg6IYIVK0v2d67PuYeQ50DfAoXy3Q8oZ6ygjNWvgb4pKWW8uHlAJowBLTgT4iGZnJAz8iSlJaVCCgGPyRkDXjFZ0wmBy23oNr0LXsf99Dpqnxz6Pk2dn_YLnH53BsdrE926Dyt8Sh61ukv47Hiek5-fLq8vvhRX3z5_vfh4VRhJayisxoqJkllT1qYGSSvDbQXQWG6gtQ0THEE30JZcS9NWUld2JmpuKXJsasbPyftx7nrTrNCa7CrqTq2jW2WrKmin_n3xbqHmYasklQJYlQe8HAeE1DuVjOvRLEzwHk2vgNJ6JnmGYITutG-1n6tl2ESfc6nl_mCbw2Gf7na7XaOQ0awRlELWvDo6i-F2g6lXK5cMdp32GDZJVXUNXMhqIOVImhhSitie7ANVQ43qvkY1dDRc3deobrLuxd_ZT6o_vWXgwwhgbmDrMA750Bu0Lg7xbHD__eK4HbMIfn7rcvRGm1-t61DxGeTVZO439Pm43w</recordid><startdate>201012</startdate><enddate>201012</enddate><creator>Wang, Jun</creator><creator>Zhang, Jianguo</creator><creator>Li, Ruiqiang</creator><creator>Zheng, Hongkun</creator><creator>Li, Jun</creator><creator>Zhang, Yong</creator><creator>Li, Heng</creator><creator>Ni, Peixiang</creator><creator>Li, Songgang</creator><creator>Li, Shengting</creator><creator>Wang, Jingqiang</creator><creator>Liu, Dongyuan</creator><creator>McDermott, Jason</creator><creator>Samudrala, Ram</creator><creator>Liu, Siqi</creator><creator>Wang, Jian</creator><creator>Yang, Huanming</creator><creator>Yu, Jun</creator><creator>Wong, Gane Ka-Shu</creator><general>Elsevier Ltd</general><general>Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark%Theoretical Life Research Center, Fudan University, Shanghai 200433, China%Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China</general><general>Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA%Computational Genomics Group, Department of Microbiology, University of Washington, Seattle, WA 98195, USA%Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China</general><general>Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton AB, T6G 2E9, Canada</general><general>Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China</general><general>Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China</general><general>Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China%Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China</general><general>Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark%Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China%Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China%Computational Genomics Group, Department of Microbiology, University of Washington, Seattle, WA 98195, USA</general><general>Elsevier</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W94</scope><scope>WU4</scope><scope>~WA</scope><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>2B.</scope><scope>4A8</scope><scope>92I</scope><scope>93N</scope><scope>PSX</scope><scope>TCJ</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>201012</creationdate><title>Evolutionary Transients in the Rice Transcriptome</title><author>Wang, Jun ; 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Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as ＂evolutionary transients＂, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.</abstract><cop>China</cop><pub>Elsevier Ltd</pub><pmid>21382590</pmid><doi>10.1016/S1672-0229(10)60023-X</doi><tpages>18</tpages><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; Elsevier ScienceDirect Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection |
| subjects | 60 APPLIED LIFE SCIENCES ARABIDOPSIS Arabidopsis - genetics BASIC BIOLOGICAL SCIENCES DNA, Complementary - genetics DNA, Plant - genetics Evolution, Molecular evolutionary transients Expressed Sequence Tags Gene Duplication Gene Expression Profiling GENES Genes, Plant Genome, Plant Oryza - genetics Oryza sativa PROTEINS RICE Sequence Analysis, DNA TRANSIENTS 双子叶植物 基因复制 核心基因 水稻基因 测试案例 转录组 |
| title | Evolutionary Transients in the Rice Transcriptome |
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