Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris)
Identifieur interne : 001780 ( Ncbi/Merge ); précédent : 001779; suivant : 001781Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris)
Auteurs : Dongying Gao [États-Unis] ; Brian Abernathy [États-Unis] ; Daniel Rohksar [États-Unis] ; Jeremy Schmutz [États-Unis] ; Scott A. Jackson [États-Unis]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2014.
Abstract
Common bean (
Url:
DOI: 10.3389/fpls.2014.00339
PubMed: 25071814
PubMed Central: 4093653
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Annotation and sequence diversity of transposable elements in common bean (<italic>Phaseolus vulgaris</italic>)</title><author><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Applied Genetic Technologies, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Abernathy, Brian" sort="Abernathy, Brian" uniqKey="Abernathy B" first="Brian" last="Abernathy">Brian Abernathy</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Applied Genetic Technologies, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Rohksar, Daniel" sort="Rohksar, Daniel" uniqKey="Rohksar D" first="Daniel" last="Rohksar">Daniel Rohksar</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>US Department of Energy Joint Genome Institute</institution><country>Walnut Creek, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>US Department of Energy Joint Genome Institute</institution><country>Walnut Creek, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>HudsonAlpha Institute of Biotechnology</institution><country>Huntsville, AL, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Applied Genetic Technologies, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25071814</idno><idno type="pmc">4093653</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4093653</idno><idno type="RBID">PMC:4093653</idno><idno type="doi">10.3389/fpls.2014.00339</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000F25</idno><idno type="wicri:Area/Pmc/Curation">000F24</idno><idno type="wicri:Area/Pmc/Checkpoint">000916</idno><idno type="wicri:Area/Ncbi/Merge">001780</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Annotation and sequence diversity of transposable elements in common bean (<italic>Phaseolus vulgaris</italic>)</title><author><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Applied Genetic Technologies, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Abernathy, Brian" sort="Abernathy, Brian" uniqKey="Abernathy B" first="Brian" last="Abernathy">Brian Abernathy</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Applied Genetic Technologies, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Rohksar, Daniel" sort="Rohksar, Daniel" uniqKey="Rohksar D" first="Daniel" last="Rohksar">Daniel Rohksar</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>US Department of Energy Joint Genome Institute</institution><country>Walnut Creek, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>US Department of Energy Joint Genome Institute</institution><country>Walnut Creek, CA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>HudsonAlpha Institute of Biotechnology</institution><country>Huntsville, AL, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Center for Applied Genetic Technologies, University of Georgia</institution><country>Athens, GA, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Common bean (<italic>Phaseolus vulgaris</italic>) is an important legume crop grown and consumed worldwide. With the availability of the common bean genome sequence, the next challenge is to annotate the genome and characterize functional DNA elements. Transposable elements (TEs) are the most abundant component of plant genomes and can dramatically affect genome evolution and genetic variation. Thus, it is pivotal to identify TEs in the common bean genome. In this study, we performed a genome-wide transposon annotation in common bean using a combination of homology and sequence structure-based methods. We developed a 2.12-Mb transposon database which includes 791 representative transposon sequences and is available upon request or from <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.org">www.phytozome.org</ext-link>. Of note, nearly all transposons in the database are previously unrecognized TEs. More than 5,000 transposon-related expressed sequence tags (ESTs) were detected which indicates that some transposons may be transcriptionally active. Two Ty1-copia retrotransposon families were found to encode the envelope-like protein which has rarely been identified in plant genomes. Also, we identified an extra open reading frame (ORF) termed ORF2 from 15 Ty3-gypsy families that was located between the ORF encoding the retrotransposase and the 3′LTR. The ORF2 was in opposite transcriptional orientation to retrotransposase. Sequence homology searches and phylogenetic analysis suggested that the ORF2 may have an ancient origin, but its function is not clear. These transposon data provide a useful resource for understanding the genome organization and evolution and may be used to identify active TEs for developing transposon-tagging system in common bean and other related genomes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abdelnoor, R V" uniqKey="Abdelnoor R">R. V. Abdelnoor</name></author><author><name sortKey="Christensen, A C" uniqKey="Christensen A">A. C. Christensen</name></author><author><name sortKey="Mohammed, S" uniqKey="Mohammed S">S. 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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 Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25071814</article-id><article-id pub-id-type="pmc">4093653</article-id><article-id pub-id-type="doi">10.3389/fpls.2014.00339</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Original Research Article</subject></subj-group></subj-group></article-categories><title-group><article-title>Annotation and sequence diversity of transposable elements in common bean (<italic>Phaseolus vulgaris</italic>)</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Gao</surname><given-names>Dongying</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/50696"></uri></contrib><contrib contrib-type="author"><name><surname>Abernathy</surname><given-names>Brian</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/171675"></uri></contrib><contrib contrib-type="author"><name><surname>Rohksar</surname><given-names>Daniel</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Schmutz</surname><given-names>Jeremy</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/171655"></uri></contrib><contrib contrib-type="author"><name><surname>Jackson</surname><given-names>Scott A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/22459"></uri></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Center for Applied Genetic Technologies, University of Georgia</institution><country>Athens, GA, USA</country></aff><aff id="aff2"><sup>2</sup><institution>US Department of Energy Joint Genome Institute</institution><country>Walnut Creek, CA, USA</country></aff><aff id="aff3"><sup>3</sup><institution>HudsonAlpha Institute of Biotechnology</institution><country>Huntsville, AL, USA</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>Rajeev K. Varshney, International Crops Research Institute for the Semi-Arid Tropics, India</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Eduard Akhunov, Kansas State University, USA; Kyujung Van, Seoul National University, South Korea</italic></p></fn><corresp id="fn002">*Correspondence: <italic>Scott A. Jackson, Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA e-mail: <email xlink:type="simple">sjackson@uga.edu</email></italic></corresp><fn fn-type="other" id="fn001"><p>This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science.</p></fn></author-notes><pub-date pub-type="epub"><day>11</day><month>7</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>5</volume><elocation-id>339</elocation-id><history><date date-type="received"><day>03</day><month>6</month><year>2014</year></date><date date-type="accepted"><day>25</day><month>6</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Gao, Abernathy, Rohksar, Schmutz and Jackson.</copyright-statement><copyright-year>2014</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p> This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>Common bean (<italic>Phaseolus vulgaris</italic>) is an important legume crop grown and consumed worldwide. With the availability of the common bean genome sequence, the next challenge is to annotate the genome and characterize functional DNA elements. Transposable elements (TEs) are the most abundant component of plant genomes and can dramatically affect genome evolution and genetic variation. Thus, it is pivotal to identify TEs in the common bean genome. In this study, we performed a genome-wide transposon annotation in common bean using a combination of homology and sequence structure-based methods. We developed a 2.12-Mb transposon database which includes 791 representative transposon sequences and is available upon request or from <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.org">www.phytozome.org</ext-link>. Of note, nearly all transposons in the database are previously unrecognized TEs. More than 5,000 transposon-related expressed sequence tags (ESTs) were detected which indicates that some transposons may be transcriptionally active. Two Ty1-copia retrotransposon families were found to encode the envelope-like protein which has rarely been identified in plant genomes. Also, we identified an extra open reading frame (ORF) termed ORF2 from 15 Ty3-gypsy families that was located between the ORF encoding the retrotransposase and the 3′LTR. The ORF2 was in opposite transcriptional orientation to retrotransposase. Sequence homology searches and phylogenetic analysis suggested that the ORF2 may have an ancient origin, but its function is not clear. These transposon data provide a useful resource for understanding the genome organization and evolution and may be used to identify active TEs for developing transposon-tagging system in common bean and other related genomes.</p></abstract><kwd-group><kwd>transposon</kwd><kwd>common bean</kwd><kwd>transposon database</kwd><kwd>evolution</kwd><kwd>ORF2</kwd></kwd-group><counts><fig-count count="4"></fig-count><table-count count="2"></table-count><equation-count count="0"></equation-count><ref-count count="42"></ref-count><page-count count="9"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name></noRegion><name sortKey="Abernathy, Brian" sort="Abernathy, Brian" uniqKey="Abernathy B" first="Brian" last="Abernathy">Brian Abernathy</name><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><name sortKey="Rohksar, Daniel" sort="Rohksar, Daniel" uniqKey="Rohksar D" first="Daniel" last="Rohksar">Daniel Rohksar</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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