LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice

<p>Abstract</p> <p>Background</p> <p>Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary...

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Main Authors: Xu Zhao, Wang Hao, Yu Hongjie
Format: Article
Language:English
Published: BMC 2008-11-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/9/565
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spelling doaj-3414ad898eca44dd8a9559046a9acbd62020-11-24T21:24:56ZengBMCBMC Genomics1471-21642008-11-019156510.1186/1471-2164-9-565LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated riceXu ZhaoWang HaoYu Hongjie<p>Abstract</p> <p>Background</p> <p>Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history.</p> <p>Results</p> <p>The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of <it>O. sativa ssp. indica </it>and that of <it>japonica </it>diverged about 600,000 years ago.</p> <p>Conclusion</p> <p>A new LTR retrotransposon identification method integrating both comparative genomics and <it>ab initio </it>algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome.</p> http://www.biomedcentral.com/1471-2164/9/565
collection DOAJ
language English
format Article
sources DOAJ
author Xu Zhao
Wang Hao
Yu Hongjie
spellingShingle Xu Zhao
Wang Hao
Yu Hongjie
LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
BMC Genomics
author_facet Xu Zhao
Wang Hao
Yu Hongjie
author_sort Xu Zhao
title LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
title_short LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
title_full LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
title_fullStr LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
title_full_unstemmed LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
title_sort ltr retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in asian cultivated rice
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2008-11-01
description <p>Abstract</p> <p>Background</p> <p>Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history.</p> <p>Results</p> <p>The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of <it>O. sativa ssp. indica </it>and that of <it>japonica </it>diverged about 600,000 years ago.</p> <p>Conclusion</p> <p>A new LTR retrotransposon identification method integrating both comparative genomics and <it>ab initio </it>algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome.</p>
url http://www.biomedcentral.com/1471-2164/9/565
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AT wanghao ltrretrotransposonsrevealrecentextensiveintersubspeciesnonreciprocalrecombinationinasiancultivatedrice
AT yuhongjie ltrretrotransposonsrevealrecentextensiveintersubspeciesnonreciprocalrecombinationinasiancultivatedrice
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