Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes
It is often anticipated that many of today's diploid plant species are in fact paleopolyploids. Given that an ancient large-scale duplication will result in an excess of relatively old duplicated genes with similar ages, we analyzed the timing of duplication of pairs of paralogous genes in 14 m...
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| Veröffentlicht in: | The Plant cell 2004-07, Vol.16 (7), p.1667-1678 |
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| creator | Blanc, G Wolfe, K.H |
| description | It is often anticipated that many of today's diploid plant species are in fact paleopolyploids. Given that an ancient large-scale duplication will result in an excess of relatively old duplicated genes with similar ages, we analyzed the timing of duplication of pairs of paralogous genes in 14 model plant species. Using EST contigs (unigenes), we identified pairs of paralogous genes in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication. For nine of the investigated species (wheat [Triticum aestivum], maize [Zea mays], tetraploid cotton [Gossypium hirsutum], diploid cotton [G. arboretum], tomato [Lycopersicon esculentum], potato [Solanum tuberosum], soybean [Glycine max], barrel medic [Medicago truncatula], and Arabidopsis thaliana), the age distributions of duplicated genes contain peaks corresponding to short evolutionary periods during which large numbers of duplicated genes were accumulated. Large-scale duplications (polyploidy or aneuploidy) are strongly suspected to be the cause of these temporal peaks of gene duplication. However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered. |
| doi_str_mv | 10.1105/tpc.021345 |
| format | Article |
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Given that an ancient large-scale duplication will result in an excess of relatively old duplicated genes with similar ages, we analyzed the timing of duplication of pairs of paralogous genes in 14 model plant species. Using EST contigs (unigenes), we identified pairs of paralogous genes in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication. For nine of the investigated species (wheat [Triticum aestivum], maize [Zea mays], tetraploid cotton [Gossypium hirsutum], diploid cotton [G. arboretum], tomato [Lycopersicon esculentum], potato [Solanum tuberosum], soybean [Glycine max], barrel medic [Medicago truncatula], and Arabidopsis thaliana), the age distributions of duplicated genes contain peaks corresponding to short evolutionary periods during which large numbers of duplicated genes were accumulated. Large-scale duplications (polyploidy or aneuploidy) are strongly suspected to be the cause of these temporal peaks of gene duplication. However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered.</description><identifier>ISSN: 1040-4651</identifier><identifier>ISSN: 1532-298X</identifier><identifier>EISSN: 1532-298X</identifier><identifier>DOI: 10.1105/tpc.021345</identifier><identifier>PMID: 15208399</identifier><language>eng</language><publisher>England: American Society of Plant Biologists</publisher><subject>Alfalfa ; Arabidopsis thaliana ; Computational Biology ; Corn ; Cotton ; crops ; Datasets ; duplicate genes ; Evolution ; Evolution, Molecular ; Expressed Sequence Tags ; Gene Duplication ; Genes ; Genes, Plant ; genetic variation ; genome ; Genome, Plant ; Genomes ; Glycine max ; Lycopersicon esculentum ; paralogous genes ; Phylogeny ; Plant cells ; plant genetics ; Plant species ; Plants ; Plants - genetics ; Polyploidy ; Rice ; sequence homology ; Soybeans ; synonymous nucleotide substitution ; Tomatoes ; Triticum aestivum ; Wheat</subject><ispartof>The Plant cell, 2004-07, Vol.16 (7), p.1667-1678</ispartof><rights>Copyright 2004 American Society of Plant Biologists</rights><rights>Copyright American Society of Plant Physiologists Jul 2004</rights><rights>Copyright © 2004, American Society of Plant Biologists 2004</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c575t-db27a8b1a6cc3a6ffdbbffa3a669d418c9e0e979a00bd3ba295a5ae9fdcf29fe3</citedby><cites>FETCH-LOGICAL-c575t-db27a8b1a6cc3a6ffdbbffa3a669d418c9e0e979a00bd3ba295a5ae9fdcf29fe3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/3872174$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/3872174$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,780,784,803,885,27915,27916,58008,58241</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15208399$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Blanc, G</creatorcontrib><creatorcontrib>Wolfe, K.H</creatorcontrib><title>Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes</title><title>The Plant cell</title><addtitle>Plant Cell</addtitle><description>It is often anticipated that many of today's diploid plant species are in fact paleopolyploids. Given that an ancient large-scale duplication will result in an excess of relatively old duplicated genes with similar ages, we analyzed the timing of duplication of pairs of paralogous genes in 14 model plant species. Using EST contigs (unigenes), we identified pairs of paralogous genes in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication. For nine of the investigated species (wheat [Triticum aestivum], maize [Zea mays], tetraploid cotton [Gossypium hirsutum], diploid cotton [G. arboretum], tomato [Lycopersicon esculentum], potato [Solanum tuberosum], soybean [Glycine max], barrel medic [Medicago truncatula], and Arabidopsis thaliana), the age distributions of duplicated genes contain peaks corresponding to short evolutionary periods during which large numbers of duplicated genes were accumulated. Large-scale duplications (polyploidy or aneuploidy) are strongly suspected to be the cause of these temporal peaks of gene duplication. However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered.</description><subject>Alfalfa</subject><subject>Arabidopsis thaliana</subject><subject>Computational Biology</subject><subject>Corn</subject><subject>Cotton</subject><subject>crops</subject><subject>Datasets</subject><subject>duplicate genes</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Expressed Sequence Tags</subject><subject>Gene Duplication</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>genetic variation</subject><subject>genome</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Glycine max</subject><subject>Lycopersicon esculentum</subject><subject>paralogous genes</subject><subject>Phylogeny</subject><subject>Plant cells</subject><subject>plant genetics</subject><subject>Plant species</subject><subject>Plants</subject><subject>Plants - genetics</subject><subject>Polyploidy</subject><subject>Rice</subject><subject>sequence homology</subject><subject>Soybeans</subject><subject>synonymous nucleotide substitution</subject><subject>Tomatoes</subject><subject>Triticum aestivum</subject><subject>Wheat</subject><issn>1040-4651</issn><issn>1532-298X</issn><issn>1532-298X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkTuP1TAQhSMEYh_QUCOwtqBAyuJHnMQFBVrxklaigBV01sQeX3yVxMZOkO6_x6tcLY-GyiOfb0Zz5lTVE0YvGaPy1RLNJeVMNPJedcqk4DVX_bf7paYNrZtWspPqLOc9pZR1TD2sTpjktBdKnVb2q7eYY0KwJMKIIYbxEMfg7YH4mUzB4kjiCPNCckTjMZdvhymhJS6FicAOifV5SX5YFx_mTIIjdo2jN7Ag2eGM-VH1wMGY8fHxPa9u3r39cvWhvv70_uPVm-vayE4utR14B_3AoDVGQOucHQbnoJStsg3rjUKKqlNA6WDFAFxJkIDKWeO4cijOq9fb3LgOE1qD85Jg1DH5CdJBB_D6b2X23_Uu_NSSNeUkpf_FsT-FHyvmRU8-GxyLfQxr1m3b9qKh4r8g61SvuLwFL_4B92FNczmC5qzvelpGFujlBpkUck7o7jZmVN8mrEvCeku4wM_-9PgbPUZagKcbsM9LSHe66DvOuqbIzzfZQdCwSz7rm8-cMkGpahgv5n4BVDa4TQ</recordid><startdate>20040701</startdate><enddate>20040701</enddate><creator>Blanc, G</creator><creator>Wolfe, K.H</creator><general>American Society of Plant Biologists</general><scope>FBQ</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>3V.</scope><scope>4T-</scope><scope>7QO</scope><scope>7TM</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>S0X</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20040701</creationdate><title>Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes</title><author>Blanc, G ; Wolfe, K.H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c575t-db27a8b1a6cc3a6ffdbbffa3a669d418c9e0e979a00bd3ba295a5ae9fdcf29fe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Alfalfa</topic><topic>Arabidopsis thaliana</topic><topic>Computational Biology</topic><topic>Corn</topic><topic>Cotton</topic><topic>crops</topic><topic>Datasets</topic><topic>duplicate genes</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Expressed Sequence Tags</topic><topic>Gene Duplication</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>genetic variation</topic><topic>genome</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>Glycine max</topic><topic>Lycopersicon esculentum</topic><topic>paralogous genes</topic><topic>Phylogeny</topic><topic>Plant cells</topic><topic>plant genetics</topic><topic>Plant species</topic><topic>Plants</topic><topic>Plants - genetics</topic><topic>Polyploidy</topic><topic>Rice</topic><topic>sequence homology</topic><topic>Soybeans</topic><topic>synonymous nucleotide substitution</topic><topic>Tomatoes</topic><topic>Triticum aestivum</topic><topic>Wheat</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Blanc, G</creatorcontrib><creatorcontrib>Wolfe, K.H</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Docstoc</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Health and Medical</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Science Journals</collection><collection>ProQuest Biological Science Journals</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>SIRS Editorial</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The Plant cell</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Blanc, G</au><au>Wolfe, K.H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes</atitle><jtitle>The Plant cell</jtitle><addtitle>Plant Cell</addtitle><date>2004-07-01</date><risdate>2004</risdate><volume>16</volume><issue>7</issue><spage>1667</spage><epage>1678</epage><pages>1667-1678</pages><issn>1040-4651</issn><issn>1532-298X</issn><eissn>1532-298X</eissn><abstract>It is often anticipated that many of today's diploid plant species are in fact paleopolyploids. Given that an ancient large-scale duplication will result in an excess of relatively old duplicated genes with similar ages, we analyzed the timing of duplication of pairs of paralogous genes in 14 model plant species. Using EST contigs (unigenes), we identified pairs of paralogous genes in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication. For nine of the investigated species (wheat [Triticum aestivum], maize [Zea mays], tetraploid cotton [Gossypium hirsutum], diploid cotton [G. arboretum], tomato [Lycopersicon esculentum], potato [Solanum tuberosum], soybean [Glycine max], barrel medic [Medicago truncatula], and Arabidopsis thaliana), the age distributions of duplicated genes contain peaks corresponding to short evolutionary periods during which large numbers of duplicated genes were accumulated. Large-scale duplications (polyploidy or aneuploidy) are strongly suspected to be the cause of these temporal peaks of gene duplication. However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered.</abstract><cop>England</cop><pub>American Society of Plant Biologists</pub><pmid>15208399</pmid><doi>10.1105/tpc.021345</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Alfalfa Arabidopsis thaliana Computational Biology Corn Cotton crops Datasets duplicate genes Evolution Evolution, Molecular Expressed Sequence Tags Gene Duplication Genes Genes, Plant genetic variation genome Genome, Plant Genomes Glycine max Lycopersicon esculentum paralogous genes Phylogeny Plant cells plant genetics Plant species Plants Plants - genetics Polyploidy Rice sequence homology Soybeans synonymous nucleotide substitution Tomatoes Triticum aestivum Wheat |
| title | Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes |
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