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Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae.

Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, Panaud O - BMC Evol. Biol. (2009)

Bottom Line: In addition, we show that it has remained active after these transfers.This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements.We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.

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Affiliation: Laboratoire Génome et Développement des Plantes, UMR CNRS/IRD/UPVD, Université de Perpignan, 52, avenue Paul Alduy, 66860 Perpignan, cedex, France. anne.roulin@univ_perp.fr

ABSTRACT

Background: Horizontal transfers (HTs) refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs) in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum), as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae.

Results: We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers.

Conclusion: This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.

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Dot plot analysis. Horizontal: O. sativa ssp. japonica. Vertical: O. sativa ssp. indica. The red square corresponds to Route66 sequence. Left border of Route66 is highly conserved between indica and japonica.
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Figure 1: Dot plot analysis. Horizontal: O. sativa ssp. japonica. Vertical: O. sativa ssp. indica. The red square corresponds to Route66 sequence. Left border of Route66 is highly conserved between indica and japonica.

Mentions: In a previous study [17], we identified Route66, an LTR-retrotransposon which is found in two copies in the genome of the cultivated rice species, Oryza sativa ssp. Japonica. One is located on chromosome 2 (nt 1 767 933 to nt 1 772 818, referred to hereafter as Osj2) and the other on chromosome 6 (nt 25 706 265 to nt 25 701 456, referred to hereafter as Osj1). Route66 is a 4,890 bp long LTR-retrotransposon with short 203 bp LTRs. In addition, only one copy of Route66 is found in the genome of the indica-type variety 93–11. The copy of Route66 of Oryza sativa ssp. japonica located on chromosome 2 is 99.5% identical to that of indica. Dot plot analyses (Figure 1) show that the japonica and indica sub-species share the insertion of Route66 on chromosome 2, which implies that either this insertion predates the radiation of the two subspecies or that it was introgressed from one subspecies into the other.


Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae.

Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, Panaud O - BMC Evol. Biol. (2009)

Dot plot analysis. Horizontal: O. sativa ssp. japonica. Vertical: O. sativa ssp. indica. The red square corresponds to Route66 sequence. Left border of Route66 is highly conserved between indica and japonica.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2664808&req=5

Figure 1: Dot plot analysis. Horizontal: O. sativa ssp. japonica. Vertical: O. sativa ssp. indica. The red square corresponds to Route66 sequence. Left border of Route66 is highly conserved between indica and japonica.
Mentions: In a previous study [17], we identified Route66, an LTR-retrotransposon which is found in two copies in the genome of the cultivated rice species, Oryza sativa ssp. Japonica. One is located on chromosome 2 (nt 1 767 933 to nt 1 772 818, referred to hereafter as Osj2) and the other on chromosome 6 (nt 25 706 265 to nt 25 701 456, referred to hereafter as Osj1). Route66 is a 4,890 bp long LTR-retrotransposon with short 203 bp LTRs. In addition, only one copy of Route66 is found in the genome of the indica-type variety 93–11. The copy of Route66 of Oryza sativa ssp. japonica located on chromosome 2 is 99.5% identical to that of indica. Dot plot analyses (Figure 1) show that the japonica and indica sub-species share the insertion of Route66 on chromosome 2, which implies that either this insertion predates the radiation of the two subspecies or that it was introgressed from one subspecies into the other.

Bottom Line: In addition, we show that it has remained active after these transfers.This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements.We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire Génome et Développement des Plantes, UMR CNRS/IRD/UPVD, Université de Perpignan, 52, avenue Paul Alduy, 66860 Perpignan, cedex, France. anne.roulin@univ_perp.fr

ABSTRACT

Background: Horizontal transfers (HTs) refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs) in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum), as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae.

Results: We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers.

Conclusion: This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.

Show MeSH
Related in: MedlinePlus