Unleashing the Genome of Brassica Rapa
Identifieur interne : 000542 ( Pmc/Curation ); précédent : 000541; suivant : 000543Unleashing the Genome of Brassica Rapa
Auteurs : Haibao Tang [États-Unis] ; Eric Lyons [États-Unis]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2012.
Abstract
The completion and release of the
Url:
DOI: 10.3389/fpls.2012.00172
PubMed: 22866056
PubMed Central: 3408644
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Unleashing the Genome of <italic>Brassica Rapa</italic></title><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>J. Craig Venter Institute</institution><country>Rockville, MD, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>iPlant Collaborative, School of Plant Sciences, University of Arizona</institution><country>Tucson, AZ, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22866056</idno><idno type="pmc">3408644</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408644</idno><idno type="RBID">PMC:3408644</idno><idno type="doi">10.3389/fpls.2012.00172</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000542</idno><idno type="wicri:Area/Pmc/Curation">000542</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Unleashing the Genome of <italic>Brassica Rapa</italic></title><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>J. Craig Venter Institute</institution><country>Rockville, MD, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>iPlant Collaborative, School of Plant Sciences, University of Arizona</institution><country>Tucson, AZ, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The completion and release of the <italic>Brassica rapa</italic> genome is of great benefit to researchers of the Brassicas, <italic>Arabidopsis</italic>, and genome evolution. While its lineage is closely related to the model organism <italic>Arabidopsis thaliana</italic>, the Brassicas experienced a whole genome triplication subsequent to their divergence. This event contemporaneously created three copies of its ancestral genome, which had diploidized through the process of homeologous gene loss known as fractionation. By the fractionation of homeologous gene content and genetic regulatory binding sites, <italic>Brassica</italic>’s genome is well placed to use comparative genomic techniques to identify syntenic regions, homeologous gene duplications, and putative regulatory sequences. Here, we use the comparative genomics platform CoGe to perform several different genomic analyses with which to study structural changes of its genome and dynamics of various genetic elements. Starting with whole genome comparisons, the <italic>Brassica</italic> paleohexaploidy is characterized, syntenic regions with <italic>A. thaliana</italic> are identified, and the TOC1 gene in the circadian rhythm pathway from <italic>A. thaliana</italic> is used to find duplicated orthologs in <italic>B. rapa</italic>. These TOC1 genes are further analyzed to identify conserved non-coding sequences that contain cis-acting regulatory elements and promoter sequences previously implicated in circadian rhythmicity. Each “cookbook style” analysis includes a step-by-step walk-through with links to CoGe to quickly reproduce each step of the analytical process.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alabadi, D" uniqKey="Alabadi D">D. Alabadí</name></author><author><name sortKey="Oyama, T" uniqKey="Oyama T">T. Oyama</name></author><author><name sortKey="Yanovsky, M J" uniqKey="Yanovsky M">M. J. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Research Foundation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22866056</article-id><article-id pub-id-type="pmc">3408644</article-id><article-id pub-id-type="doi">10.3389/fpls.2012.00172</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Methods Article</subject></subj-group></subj-group></article-categories><title-group><article-title>Unleashing the Genome of <italic>Brassica Rapa</italic></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tang</surname><given-names>Haibao</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lyons</surname><given-names>Eric</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="fn001">*</xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>J. Craig Venter Institute</institution><country>Rockville, MD, USA</country></aff><aff id="aff2"><sup>2</sup><institution>iPlant Collaborative, School of Plant Sciences, University of Arizona</institution><country>Tucson, AZ, USA</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Michael Freeling, University of California Berkeley, USA</p></fn><fn fn-type="edited-by"><p>Reviewed by: Michael Freeling, University of California Berkeley, USA; Xiangfeng Wang, University of Arizona, USA</p></fn><corresp id="fn001">*Correspondence: Eric Lyons, iPlant Collaborative, School of Plant Sciences, University of Arizona, Keating Bioresearch Building, 1657 E. Helen St. Tucson, AZ 85745, USA. e-mail: <email>elyons.uoa@gmail.com</email></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Frontiers in Plant Genetics and Genomics, a specialty of Frontiers in Plant Science.</p></fn></author-notes><pub-date pub-type="epub"><day>31</day><month>7</month><year>2012</year></pub-date><pub-date pub-type="collection"><year>2012</year></pub-date><volume>3</volume><elocation-id>172</elocation-id><history><date date-type="received"><day>31</day><month>5</month><year>2012</year></date><date date-type="accepted"><day>12</day><month>7</month><year>2012</year></date></history><permissions><copyright-statement>Copyright © 2012 Tang and Lyons.</copyright-statement><copyright-year>2012</copyright-year><license license-type="open-access" xlink:href="http://www.frontiersin.org/licenseagreement"><license-p>This is an open-access article distributed under the terms of the <uri xlink:type="simple" xlink:href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution License</uri>, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.</license-p></license></permissions><abstract><p>The completion and release of the <italic>Brassica rapa</italic> genome is of great benefit to researchers of the Brassicas, <italic>Arabidopsis</italic>, and genome evolution. While its lineage is closely related to the model organism <italic>Arabidopsis thaliana</italic>, the Brassicas experienced a whole genome triplication subsequent to their divergence. This event contemporaneously created three copies of its ancestral genome, which had diploidized through the process of homeologous gene loss known as fractionation. By the fractionation of homeologous gene content and genetic regulatory binding sites, <italic>Brassica</italic>’s genome is well placed to use comparative genomic techniques to identify syntenic regions, homeologous gene duplications, and putative regulatory sequences. Here, we use the comparative genomics platform CoGe to perform several different genomic analyses with which to study structural changes of its genome and dynamics of various genetic elements. Starting with whole genome comparisons, the <italic>Brassica</italic> paleohexaploidy is characterized, syntenic regions with <italic>A. thaliana</italic> are identified, and the TOC1 gene in the circadian rhythm pathway from <italic>A. thaliana</italic> is used to find duplicated orthologs in <italic>B. rapa</italic>. These TOC1 genes are further analyzed to identify conserved non-coding sequences that contain cis-acting regulatory elements and promoter sequences previously implicated in circadian rhythmicity. Each “cookbook style” analysis includes a step-by-step walk-through with links to CoGe to quickly reproduce each step of the analytical process.</p></abstract><kwd-group><kwd>comparative genomics</kwd><kwd>synteny</kwd><kwd>CoGe</kwd><kwd><italic>Brassica rapa</italic></kwd><kwd>syntenic dotplot</kwd><kwd><italic>Arabidopsis</italic></kwd><kwd>TOC1</kwd><kwd>conserved non-coding sequences</kwd></kwd-group><counts><fig-count count="6"></fig-count><table-count count="0"></table-count><equation-count count="0"></equation-count><ref-count count="67"></ref-count><page-count count="12"></page-count><word-count count="9886"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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