Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

Gao, Lizhi; McCarthy, Eugene M.; Ganko, Eric W.; McDonald, John F.

Title:

Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

dc.contributor.author	Gao, Lizhi	en_US
dc.contributor.author	McCarthy, Eugene M.	en_US
dc.contributor.author	Ganko, Eric W.	en_US
dc.contributor.author	McDonald, John F.	en_US
dc.contributor.corporatename	University of Georgia. Dept. of Genetics	en_US
dc.date.accessioned	2010-03-19T20:54:37Z
dc.date.available	2010-03-19T20:54:37Z
dc.date.issued	2004-03-02
dc.description	© 2004 Gao et al; licensee BioMed Central Ltd. The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2164/5/18	en
dc.description	DOI: 10.1186/1471-2164-5-18
dc.description.abstract	Background: LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results: To explore the evolutionary history of long terminal repeat (LTR) retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTRretrotransposons per Mb were detected in Chromosome 10. Conclusions: Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (< 680,000 years). LTR-retrotransposons present in the rice genome range in age from those just recently inserted up to nearly 10 million years old. Approximately 20% of LTR retrotransposon sequences lie within putative genes. The distribution of elements across chromosome 10 is non-random with the highest density (48 elements per Mb) being present in the pericentric region.	en
dc.identifier.citation	Lizhi Gao, Eugene M. McCarthy, Eric W. Ganko and John F. McDonald, "Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences," BMC Genomics 2004, 5:18	en
dc.identifier.doi	10.1186/1471-2164-5-18
dc.identifier.issn	1471-2164
dc.identifier.uri	http://hdl.handle.net/1853/32452
dc.language.iso	en_US	en
dc.publisher	Georgia Institute of Technology	en
dc.publisher.original	BioMed Central
dc.subject	Retrotransposons	en
dc.subject	Eukaryotic genomes	en
dc.subject	Long terminal repeat retrotransposons	en
dc.subject	LTR	en
dc.subject	Oryza sativa	en
dc.subject	Rice	en
dc.title	Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences	en
dc.type	Text
dc.type.genre	Article
dspace.entity.type	Publication
local.contributor.author	McDonald, John F.
local.contributor.corporatename	College of Sciences
local.contributor.corporatename	School of Biological Sciences
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