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Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza

Identifieur interne : 000049 ( Main/Curation ); précédent : 000048; suivant : 000050

Structural 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 :

RBID : PMC:4718150

Abstract

Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs 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 RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93–11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, RTPOSON, might have an impact on genome evolution, genic innovation, and genetic variation.


Url:
DOI: 10.4137/EBO.S35158
PubMed: 26819544
PubMed Central: 4718150

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PMC:4718150

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<name sortKey="Hsu, Yu Chia" sort="Hsu, Yu Chia" uniqKey="Hsu Y" first="Yu-Chia" last="Hsu">Yu-Chia Hsu</name>
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<nlm:aff id="af1-ebo-12-2016-029">Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan.</nlm:aff>
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<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>
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