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

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

doi:10.1186/1471-2164-5-18

Abstract

BackgroundLTR 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.ResultsTo 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 LTR-retrotransposons per Mb were detected in Chromosome 10.ConclusionsGypsy-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.

Highlights

long terminal repeat (LTR) Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes far examined
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)
Four additional groups of nonautonomous LTR retrotransposons identified in this previous study did not display a reverse transcriptase (RTs) sequence homology but were, designated as families based on their distinct structures [32]

Summary

Introduction

LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes far examined. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. In particular, have been found to be comprised of a remarkably high number of LTR retrotransposons [2,3,4]. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in both animals and plants [4,7,8,9,10,11,12,13]. The recent release of draft genome sequences of two rice subspecies, indica [22] and japonica [23], and ongoing efforts to compile a complete japonica rice genome sequence publicly available by International Rice Genome Sequencing Project (IRGSP) [15], promises to greatly facilitate the study of rice genome evolution

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