HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes
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Auteurs : Wenwei Xiong ; Limei He ; Jinsheng Lai [République populaire de Chine] ; Hugo K. Dooner ; Chunguang DuSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2014.
Abstract
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DOI: 10.1073/pnas.1410068111
PubMed: 24982153
PubMed Central: 4104883
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">HelitronScanner uncovers a large overlooked cache of <italic>Helitron</italic> transposons in many plant genomes</title><author><name sortKey="Xiong, Wenwei" sort="Xiong, Wenwei" uniqKey="Xiong W" first="Wenwei" last="Xiong">Wenwei Xiong</name><affiliation><nlm:aff id="aff1">Department of Biology and Molecular Biology,<institution>Montclair State University</institution>, Montclair,<addr-line>NJ</addr-line> 07043;</nlm:aff></affiliation></author><author><name sortKey="He, Limei" sort="He, Limei" uniqKey="He L" first="Limei" last="He">Limei He</name><affiliation><nlm:aff id="aff2">Waksman Institute,<institution>Rutgers, the State University of New Jersey</institution>, Piscataway,<addr-line>NJ</addr-line> 08854;</nlm:aff></affiliation></author><author><name sortKey="Lai, Jinsheng" sort="Lai, Jinsheng" uniqKey="Lai J" first="Jinsheng" last="Lai">Jinsheng Lai</name><affiliation wicri:level="1"><nlm:aff wicri:cut="; and" id="aff3">National Maize Improvement Center,<institution>China Agricultural University</institution>, Beijing 100083,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dooner, Hugo K" sort="Dooner, Hugo K" uniqKey="Dooner H" first="Hugo K." last="Dooner">Hugo K. Dooner</name><affiliation><nlm:aff id="aff2">Waksman Institute,<institution>Rutgers, the State University of New Jersey</institution>, Piscataway,<addr-line>NJ</addr-line> 08854;</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Department of Plant Biology,<institution>Rutgers, the State University of New Jersey</institution>, New Brunswick,<addr-line>NJ</addr-line> 08801</nlm:aff></affiliation></author><author><name sortKey="Du, Chunguang" sort="Du, Chunguang" uniqKey="Du C" first="Chunguang" last="Du">Chunguang Du</name><affiliation><nlm:aff id="aff1">Department of Biology and Molecular Biology,<institution>Montclair State University</institution>, Montclair,<addr-line>NJ</addr-line> 07043;</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24982153</idno><idno type="pmc">4104883</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104883</idno><idno type="RBID">PMC:4104883</idno><idno type="doi">10.1073/pnas.1410068111</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000D40</idno><idno type="wicri:Area/Pmc/Curation">000D39</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">HelitronScanner uncovers a large overlooked cache of <italic>Helitron</italic> transposons in many plant genomes</title><author><name sortKey="Xiong, Wenwei" sort="Xiong, Wenwei" uniqKey="Xiong W" first="Wenwei" last="Xiong">Wenwei Xiong</name><affiliation><nlm:aff id="aff1">Department of Biology and Molecular Biology,<institution>Montclair State University</institution>, Montclair,<addr-line>NJ</addr-line> 07043;</nlm:aff></affiliation></author><author><name sortKey="He, Limei" sort="He, Limei" uniqKey="He L" first="Limei" last="He">Limei He</name><affiliation><nlm:aff id="aff2">Waksman Institute,<institution>Rutgers, the State University of New Jersey</institution>, Piscataway,<addr-line>NJ</addr-line> 08854;</nlm:aff></affiliation></author><author><name sortKey="Lai, Jinsheng" sort="Lai, Jinsheng" uniqKey="Lai J" first="Jinsheng" last="Lai">Jinsheng Lai</name><affiliation wicri:level="1"><nlm:aff wicri:cut="; and" id="aff3">National Maize Improvement Center,<institution>China Agricultural University</institution>, Beijing 100083,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Dooner, Hugo K" sort="Dooner, Hugo K" uniqKey="Dooner H" first="Hugo K." last="Dooner">Hugo K. Dooner</name><affiliation><nlm:aff id="aff2">Waksman Institute,<institution>Rutgers, the State University of New Jersey</institution>, Piscataway,<addr-line>NJ</addr-line> 08854;</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Department of Plant Biology,<institution>Rutgers, the State University of New Jersey</institution>, New Brunswick,<addr-line>NJ</addr-line> 08801</nlm:aff></affiliation></author><author><name sortKey="Du, Chunguang" sort="Du, Chunguang" uniqKey="Du C" first="Chunguang" last="Du">Chunguang Du</name><affiliation><nlm:aff id="aff1">Department of Biology and Molecular Biology,<institution>Montclair State University</institution>, Montclair,<addr-line>NJ</addr-line> 07043;</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Significance</title><p><italic>Helitrons</italic> are unusual rolling-circle eukaryotic transposons with a remarkable ability to capture gene sequences, which makes them of considerable evolutionary importance. Because <italic>Helitrons</italic> lack typical transposon features, they are challenging to identify and are estimated to comprise at most 2% of sequenced genomes. Here, we describe HelitronScanner, a generalized tool for their identification based on a motif-extracting algorithm proposed initially in a study of natural languages. HelitronScanner overcomes the divergence of <italic>Helitron</italic> termini among species by using conserved nucleotides at potentially variable locations. Many new <italic>Helitrons</italic> were identified in all organisms examined, resulting in a major reassessment of their abundance in eukaryotic genomes. In maize, they make up >6% of the genome and are the most abundant DNA transposons identified.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24982153</article-id><article-id pub-id-type="pmc">4104883</article-id><article-id pub-id-type="publisher-id">201410068</article-id><article-id pub-id-type="doi">10.1073/pnas.1410068111</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Genetics</subject></subj-group></subj-group></article-categories><title-group><article-title>HelitronScanner uncovers a large overlooked cache of <italic>Helitron</italic> transposons in many plant genomes</article-title><alt-title alt-title-type="short">Helitron identification by local sequence patterns</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Xiong</surname><given-names>Wenwei</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>He</surname><given-names>Limei</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lai</surname><given-names>Jinsheng</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dooner</surname><given-names>Hugo K.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="aff" rid="aff4"><sup>d</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Du</surname><given-names>Chunguang</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1"><sup>a</sup>Department of Biology and Molecular Biology,<institution>Montclair State University</institution>, Montclair,<addr-line>NJ</addr-line> 07043;</aff><aff id="aff2"><sup>b</sup>Waksman Institute,<institution>Rutgers, the State University of New Jersey</institution>, Piscataway,<addr-line>NJ</addr-line> 08854;</aff><aff id="aff3"><sup>c</sup>National Maize Improvement Center,<institution>China Agricultural University</institution>, Beijing 100083,<country>China</country>; and</aff><aff id="aff4"><sup>d</sup>Department of Plant Biology,<institution>Rutgers, the State University of New Jersey</institution>, New Brunswick,<addr-line>NJ</addr-line> 08801</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence may be addressed. E-mail: <email>dooner@waksman.rutgers.edu</email> or <email>duc@mail.montclair.edu</email>.</corresp><fn fn-type="edited-by"><p>Contributed by Hugo K. Dooner, June 6, 2014 (sent for review January 28, 2014)</p></fn><fn fn-type="con"><p>Author contributions: W.X. and C.D. designed research; W.X., L.H., and C.D. performed research; J.L. contributed new reagents/analytic tools; W.X., L.H., H.K.D., and C.D. analyzed data; and W.X., H.K.D., and C.D. wrote the paper.</p></fn></author-notes><pub-date pub-type="ppub"><day>15</day><month>7</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>30</day><month>6</month><year>2014</year></pub-date><volume>111</volume><issue>28</issue><fpage>10263</fpage><lpage>10268</lpage><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201410068.pdf"></self-uri><abstract abstract-type="executive-summary"><title>Significance</title><p><italic>Helitrons</italic> are unusual rolling-circle eukaryotic transposons with a remarkable ability to capture gene sequences, which makes them of considerable evolutionary importance. Because <italic>Helitrons</italic> lack typical transposon features, they are challenging to identify and are estimated to comprise at most 2% of sequenced genomes. Here, we describe HelitronScanner, a generalized tool for their identification based on a motif-extracting algorithm proposed initially in a study of natural languages. HelitronScanner overcomes the divergence of <italic>Helitron</italic> termini among species by using conserved nucleotides at potentially variable locations. Many new <italic>Helitrons</italic> were identified in all organisms examined, resulting in a major reassessment of their abundance in eukaryotic genomes. In maize, they make up >6% of the genome and are the most abundant DNA transposons identified.</p></abstract><abstract><p>Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. <italic>Helitrons</italic> are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, <italic>Helitrons</italic> do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized <italic>Helitron</italic> identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 <italic>Helitrons</italic> from a wide range of plant genomes in a highly automated way. We tested HelitronScanner’s predictive ability in maize, a species with highly heterogeneous <italic>Helitron</italic> elements. LCV scores for the 5′ and 3′ termini of the predicted <italic>Helitrons</italic> provide a primary confidence level and element copy number provides a secondary one. Newly identified <italic>Helitrons</italic> were validated by PCR assays or by in silico comparative analysis of insertion site polymorphism among multiple accessions. Many new <italic>Helitrons</italic> were identified in model species, such as maize, rice, and <italic>Arabidopsis</italic>, and in a variety of organisms where <italic>Helitrons</italic> had not been reported previously to our knowledge, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.</p></abstract><kwd-group><kwd>transposition</kwd><kwd>algorithm</kwd><kwd>computational tool</kwd><kwd>bioinformatic analysis</kwd></kwd-group><counts><page-count count="6"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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