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

Gao L, McCarthy EM, Ganko EW, McDonald JF - BMC Genomics (2004)

Bottom Line: Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons.Gypsy-like elements were found to be >4 x more abundant than copia-like elements.Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia 30602, USA. LZGao@sph.uth.tmc.edu

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 LTR-retrotransposons per Mb were detected in Chromosome 10.

Conclusions: Gypsy-like elements were found to be >4 x 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.

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O. sativa gypsy-like LTR-retrotransposon age calculated using intraelements LTR Nucleotide Similarities (B). Only are those elements that contain LTR nucleotide divergence values other than zero included.
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Figure 5: O. sativa gypsy-like LTR-retrotransposon age calculated using intraelements LTR Nucleotide Similarities (B). Only are those elements that contain LTR nucleotide divergence values other than zero included.

Mentions: LTR nucleotide identity can be used to estimate the time of LTR retrotransposon integration [37-39]. Of the 217 full-length elements that we have identified in O. sativa, 116 (53.5%) have >99% LTR similarity with 34 of these (15.7%) being identical. The remaining 101(46.5%)have relatively low levels of nucleotide divergence (<99%). Among them, 31(14%), 24(11%), 30(14%), and 15(7%) fell into different ranges of LTR similarities of 98–99%, 97–98%, 95–97%, and <95%, respectively. Identical LTRs imply that the elements have inserted recently and have not had time to accumulate mutations between LTRs. Using the average neutral substitution rate for grasses [37,39,40] of 0.065 substitutions per site per million years and the intra-element LTR divergence calculated here, we have computed the estimated integration time of the 181 elements with LTR nucleotide divergence (Table 1, see Additional file: 1). Based on the full-length elements available in this study, we estimate over half of rice retroelements (53.5%) with >99% LTR identity have inserted within the last 770,000 years while the older elements (46.5%) have integrated over a span of 770,000–7,700,000 years ago. Figure 3, 4 and 5 show estimated ages of all the full-length elements found in our study.


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

Gao L, McCarthy EM, Ganko EW, McDonald JF - BMC Genomics (2004)

O. sativa gypsy-like LTR-retrotransposon age calculated using intraelements LTR Nucleotide Similarities (B). Only are those elements that contain LTR nucleotide divergence values other than zero included.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC373447&req=5

Figure 5: O. sativa gypsy-like LTR-retrotransposon age calculated using intraelements LTR Nucleotide Similarities (B). Only are those elements that contain LTR nucleotide divergence values other than zero included.
Mentions: LTR nucleotide identity can be used to estimate the time of LTR retrotransposon integration [37-39]. Of the 217 full-length elements that we have identified in O. sativa, 116 (53.5%) have >99% LTR similarity with 34 of these (15.7%) being identical. The remaining 101(46.5%)have relatively low levels of nucleotide divergence (<99%). Among them, 31(14%), 24(11%), 30(14%), and 15(7%) fell into different ranges of LTR similarities of 98–99%, 97–98%, 95–97%, and <95%, respectively. Identical LTRs imply that the elements have inserted recently and have not had time to accumulate mutations between LTRs. Using the average neutral substitution rate for grasses [37,39,40] of 0.065 substitutions per site per million years and the intra-element LTR divergence calculated here, we have computed the estimated integration time of the 181 elements with LTR nucleotide divergence (Table 1, see Additional file: 1). Based on the full-length elements available in this study, we estimate over half of rice retroelements (53.5%) with >99% LTR identity have inserted within the last 770,000 years while the older elements (46.5%) have integrated over a span of 770,000–7,700,000 years ago. Figure 3, 4 and 5 show estimated ages of all the full-length elements found in our study.

Bottom Line: Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons.Gypsy-like elements were found to be >4 x more abundant than copia-like elements.Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia 30602, USA. LZGao@sph.uth.tmc.edu

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 LTR-retrotransposons per Mb were detected in Chromosome 10.

Conclusions: Gypsy-like elements were found to be >4 x 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.

Show MeSH