Intron gain and loss in segmentally duplicated genes in rice
Identifieur interne : 000559 ( Pmc/Curation ); précédent : 000558; suivant : 000560Intron gain and loss in segmentally duplicated genes in rice
Auteurs : Haining Lin [États-Unis] ; Wei Zhu [États-Unis] ; Joana C. Silva [États-Unis] ; Xun Gu [États-Unis] ; C Robin Buell [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2006.
Abstract
Analysis of over 3,000 co-linear paired genes in rice shows more intron loss than intron gain following segmental duplication.
Url:
DOI: 10.1186/gb-2006-7-5-r41
PubMed: 16719932
PubMed Central: 1779517
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Silva</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Gu, Xun" sort="Gu, Xun" uniqKey="Gu X" first="Xun" last="Gu">Xun Gu</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011</wicri:regionArea></affiliation></author><author><name sortKey="Buell, C Robin" sort="Buell, C Robin" uniqKey="Buell C" first="C Robin" last="Buell">C Robin Buell</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">16719932</idno><idno type="pmc">1779517</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779517</idno><idno type="RBID">PMC:1779517</idno><idno type="doi">10.1186/gb-2006-7-5-r41</idno><date when="2006">2006</date><idno type="wicri:Area/Pmc/Corpus">000559</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000559</idno><idno type="wicri:Area/Pmc/Curation">000559</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000559</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Intron gain and loss in segmentally duplicated genes in rice</title><author><name sortKey="Lin, Haining" sort="Lin, Haining" uniqKey="Lin H" first="Haining" last="Lin">Haining Lin</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Wei" sort="Zhu, Wei" uniqKey="Zhu W" first="Wei" last="Zhu">Wei Zhu</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Silva, Joana C" sort="Silva, Joana C" uniqKey="Silva J" first="Joana C" last="Silva">Joana C. Silva</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Gu, Xun" sort="Gu, Xun" uniqKey="Gu X" first="Xun" last="Gu">Xun Gu</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011</wicri:regionArea></affiliation></author><author><name sortKey="Buell, C Robin" sort="Buell, C Robin" uniqKey="Buell C" first="C Robin" last="Buell">C Robin Buell</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2006">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Analysis of over 3,000 co-linear paired genes in rice shows more intron loss than intron gain following segmental duplication.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-title>Genome Biology</journal-title><issn pub-type="ppub">1465-6906</issn><issn pub-type="epub">1465-6914</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">16719932</article-id><article-id pub-id-type="pmc">1779517</article-id><article-id pub-id-type="publisher-id">gb-2006-7-5-r41</article-id><article-id pub-id-type="doi">10.1186/gb-2006-7-5-r41</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Intron gain and loss in segmentally duplicated genes in rice</article-title></title-group><contrib-group><contrib id="A1" contrib-type="author"><name><surname>Lin</surname><given-names>Haining</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>hlin@tigr.org</email></contrib><contrib id="A2" contrib-type="author"><name><surname>Zhu</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>wzhu@tigr.org</email></contrib><contrib id="A3" contrib-type="author"><name><surname>Silva</surname><given-names>Joana C</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>jsilva@tigr.org</email></contrib><contrib id="A4" contrib-type="author"><name><surname>Gu</surname><given-names>Xun</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>xgu@iastate.edu</email></contrib><contrib id="A5" corresp="yes" contrib-type="author"><name><surname>Buell</surname><given-names>C Robin</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>rbuell@tigr.org</email></contrib></contrib-group><aff id="I1"><label>1</label>The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA</aff><aff id="I2"><label>2</label>Department of Genetics, Development, and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA</aff><pub-date pub-type="ppub"><year>2006</year></pub-date><pub-date pub-type="epub"><day>23</day><month>5</month><year>2006</year></pub-date><volume>7</volume><issue>5</issue><fpage>R41</fpage><lpage>R41</lpage><ext-link ext-link-type="uri" xlink:href="http://genomebiology.com/2006/7/5/R41"></ext-link><history><date date-type="received"><day>30</day><month>1</month><year>2006</year></date><date date-type="rev-recd"><day>21</day><month>3</month><year>2006</year></date><date date-type="accepted"><day>24</day><month>4</month><year>2006</year></date></history><permissions><copyright-statement>Copyright © 2006 Lin et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2006</copyright-year><copyright-holder>Lin et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p><pmc-comment>
Lin
Haining
hlin@tigr.org
Intron gain and loss in segmentally duplicated genes in rice
2006 Genome Biology 7(5): R41-. (2006) 1465-6906(2006)7:5 urn:ISSN:1465-6906
</license></permissions><abstract abstract-type="short"><p>Analysis of over 3,000 co-linear paired genes in rice shows more intron loss than intron gain following segmental duplication.</p></abstract><abstract><sec><title>Background</title><p>Introns are under less selection pressure than exons, and consequently, intronic sequences have a higher rate of gain and loss than exons. In a number of plant species, a large portion of the genome has been segmentally duplicated, giving rise to a large set of duplicated genes. The recent completion of the rice genome in which segmental duplication has been documented has allowed us to investigate intron evolution within rice, a diploid monocotyledonous species.</p></sec><sec><title>Results</title><p>Analysis of segmental duplication in rice revealed that 159 Mb of the 371 Mb genome and 21,570 of the 43,719 non-transposable element-related genes were contained within a duplicated region. In these duplicated regions, 3,101 collinear paired genes were present. Using this set of segmentally duplicated genes, we investigated intron evolution from full-length cDNA-supported non-transposable element-related gene models of rice. Using gene pairs that have an ortholog in the dicotyledonous model species <italic>Arabidopsis thaliana</italic>, we identified more intron loss (49 introns within 35 gene pairs) than intron gain (5 introns within 5 gene pairs) following segmental duplication. We were unable to demonstrate preferential intron loss at the 3' end of genes as previously reported in mammalian genomes. However, we did find that the four nucleotides of exons that flank lost introns had less frequently used 4-mers.</p></sec><sec><title>Conclusion</title><p>We observed that intron evolution within rice following segmental duplication is largely dominated by intron loss. In two of the five cases of intron gain within segmentally duplicated genes, the gained sequences were similar to transposable elements.</p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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