Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza
Identifieur interne : 000049 ( Main/Curation ); précédent : 000048; suivant : 000050Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza
Auteurs : Yu-Chia Hsu [Taïwan] ; Chang-Sheng Wang [Taïwan] ; Yann-Rong Lin [Taïwan] ; Yong-Pei Wu [Taïwan]Source :
- Evolutionary Bioinformatics Online [ 1176-9343 ] ; 2016.
Abstract
Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named
Url:
DOI: 10.4137/EBO.S35158
PubMed: 26819544
PubMed Central: 4718150
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Structural Diversity of a Novel LTR Retrotransposon, <italic>RTPOSON</italic>
, in the Genus <italic>Oryza</italic>
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<author><name sortKey="Hsu, Yu Chia" sort="Hsu, Yu Chia" uniqKey="Hsu Y" first="Yu-Chia" last="Hsu">Yu-Chia Hsu</name>
<affiliation wicri:level="1"><nlm:aff id="af1-ebo-12-2016-029">Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Taïwan</country>
<wicri:regionArea>Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi</wicri:regionArea>
<wicri:noRegion>Chiayi</wicri:noRegion>
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<author><name sortKey="Wang, Chang Sheng" sort="Wang, Chang Sheng" uniqKey="Wang C" first="Chang-Sheng" last="Wang">Chang-Sheng Wang</name>
<affiliation wicri:level="1"><nlm:aff id="af2-ebo-12-2016-029">Department of Agronomy, National Chung Hsing University, Taichung, Taiwan.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Taïwan</country>
<wicri:regionArea>Department of Agronomy, National Chung Hsing University, Taichung</wicri:regionArea>
<wicri:noRegion>Taichung</wicri:noRegion>
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<author><name sortKey="Lin, Yann Rong" sort="Lin, Yann Rong" uniqKey="Lin Y" first="Yann-Rong" last="Lin">Yann-Rong Lin</name>
<affiliation wicri:level="1"><nlm:aff id="af3-ebo-12-2016-029">Department of Agronomy, National Taiwan University, Taipei, Taiwan.</nlm:aff>
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<author><name sortKey="Wu, Yong Pei" sort="Wu, Yong Pei" uniqKey="Wu Y" first="Yong-Pei" last="Wu">Yong-Pei Wu</name>
<affiliation wicri:level="1"><nlm:aff id="af1-ebo-12-2016-029">Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Taïwan</country>
<wicri:regionArea>Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi</wicri:regionArea>
<wicri:noRegion>Chiayi</wicri:noRegion>
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<series><title level="j">Evolutionary Bioinformatics Online</title>
<idno type="eISSN">1176-9343</idno>
<imprint><date when="2016">2016</date>
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<front><div type="abstract" xml:lang="en"><p>Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named <italic>RTPOSON</italic>
primarily occurs in the genus <italic>Oryza</italic>
and in several species of the Poaceae family. <italic>RTPOSON</italic>
has been identified in the <italic>Ty1-copia</italic>
group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 <italic>RTPOSONs</italic>
were identified in <italic>Oryza</italic>
genomes; 127 <italic>RTPOSONs</italic>
with LTRs and <italic>gag-pol</italic>
elements were classified into three subgroups. The subgroup <italic>RTPOSON_sub3</italic>
had the smallest DNA size and 97% (32/33) of <italic>RTPOSON</italic>
elements from <italic>Oryza punctata</italic>
are classified in this group. The insertion time of these <italic>RTPOSONs</italic>
varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5–5.0 Mya. A total of 37 different orthologous insertions of <italic>RTPOSONs</italic>
, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. <italic>japonica</italic>
cv. Nipponbare and ssp. <italic>indica</italic>
cv. 93–11. A part of intact <italic>RTPOSON</italic>
elements was evolved independently after the divergence of <italic>indica</italic>
and <italic>japonica</italic>
. In addition, intact <italic>RTPOSONs</italic>
and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, <italic>RTPOSON</italic>
, might have an impact on genome evolution, genic innovation, and genetic variation.</p>
</div>
</front>
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