HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes
Identifieur interne : 000A55 ( Main/Exploration ); précédent : 000A54; suivant : 000A56HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes
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
Url:
DOI: 10.1073/pnas.1410068111
PubMed: 24982153
PubMed Central: 4104883
Affiliations:
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Le document en format XML
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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>
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<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>
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<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>
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<author><name sortKey="Dooner, Hugo K" sort="Dooner, Hugo K" uniqKey="Dooner H" first="Hugo K." last="Dooner">Hugo K. Dooner</name>
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<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>
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<author><name sortKey="Du, Chunguang" sort="Du, Chunguang" uniqKey="Du C" first="Chunguang" last="Du">Chunguang Du</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">HelitronScanner uncovers a large overlooked cache of <italic>Helitron</italic>
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<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>
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<author><name sortKey="He, Limei" sort="He, Limei" uniqKey="He L" first="Limei" last="He">Limei He</name>
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, Piscataway,<addr-line>NJ</addr-line>
08854;</nlm:aff>
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<author><name sortKey="Lai, Jinsheng" sort="Lai, Jinsheng" uniqKey="Lai J" first="Jinsheng" last="Lai">Jinsheng Lai</name>
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, Beijing 100083,<country>China</country>
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, Piscataway,<addr-line>NJ</addr-line>
08854;</nlm:aff>
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<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>
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<author><name sortKey="Du, Chunguang" sort="Du, Chunguang" uniqKey="Du C" first="Chunguang" last="Du">Chunguang Du</name>
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, Montclair,<addr-line>NJ</addr-line>
07043;</nlm:aff>
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<series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title>
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<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>
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<name sortKey="He, Limei" sort="He, Limei" uniqKey="He L" first="Limei" last="He">Limei He</name>
<name sortKey="Xiong, Wenwei" sort="Xiong, Wenwei" uniqKey="Xiong W" first="Wenwei" last="Xiong">Wenwei Xiong</name>
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