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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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The distribution of full-length, solo and fragmented LTR elements along the chromosome 10. The borders of the pericentromeric regions of chromosome 10 were assigned as being 5 cM from the center of the centromere on each arm. The remainders of the chromosome were designated as arms. Both copia-like and gypsy-like LTR retrotransposons exhibit nonrandom clustering along the chromosome. More LTR retrotransposons reside in the pericentric regions of the chromosome than in the arms, and short arm of Chromosome 10 also displays a higher density of the elements than long arm. The number of gypsy-like elements are more than that of copia-like elements on chromosome 10.
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Figure 7: The distribution of full-length, solo and fragmented LTR elements along the chromosome 10. The borders of the pericentromeric regions of chromosome 10 were assigned as being 5 cM from the center of the centromere on each arm. The remainders of the chromosome were designated as arms. Both copia-like and gypsy-like LTR retrotransposons exhibit nonrandom clustering along the chromosome. More LTR retrotransposons reside in the pericentric regions of the chromosome than in the arms, and short arm of Chromosome 10 also displays a higher density of the elements than long arm. The number of gypsy-like elements are more than that of copia-like elements on chromosome 10.

Mentions: At the time of this study, about 48% rice genomic sequences were available in the public database, which included the almost entirely sequenced chromosome 1 and 10. In an initial effort to gain insight into the intra-chromosomal distribution of O. sativa LTR retrotransposons, we selected Chromosome 10 for a more detailed analysis. Tests were conducted to determine whether LTR retrotransposon sequences were randomly distributed on Chromosome 10. We found that the average density of elements on Chromosome 10 is 22.321/Mb (Table 3). There is a nonrandom clustering of both copia-like and gypsy-like LTR retrotransposons along the chromosome (Figure 6, 7 and 8).


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)

The distribution of full-length, solo and fragmented LTR elements along the chromosome 10. The borders of the pericentromeric regions of chromosome 10 were assigned as being 5 cM from the center of the centromere on each arm. The remainders of the chromosome were designated as arms. Both copia-like and gypsy-like LTR retrotransposons exhibit nonrandom clustering along the chromosome. More LTR retrotransposons reside in the pericentric regions of the chromosome than in the arms, and short arm of Chromosome 10 also displays a higher density of the elements than long arm. The number of gypsy-like elements are more than that of copia-like elements on chromosome 10.
© Copyright Policy
Related In: Results  -  Collection

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Figure 7: The distribution of full-length, solo and fragmented LTR elements along the chromosome 10. The borders of the pericentromeric regions of chromosome 10 were assigned as being 5 cM from the center of the centromere on each arm. The remainders of the chromosome were designated as arms. Both copia-like and gypsy-like LTR retrotransposons exhibit nonrandom clustering along the chromosome. More LTR retrotransposons reside in the pericentric regions of the chromosome than in the arms, and short arm of Chromosome 10 also displays a higher density of the elements than long arm. The number of gypsy-like elements are more than that of copia-like elements on chromosome 10.
Mentions: At the time of this study, about 48% rice genomic sequences were available in the public database, which included the almost entirely sequenced chromosome 1 and 10. In an initial effort to gain insight into the intra-chromosomal distribution of O. sativa LTR retrotransposons, we selected Chromosome 10 for a more detailed analysis. Tests were conducted to determine whether LTR retrotransposon sequences were randomly distributed on Chromosome 10. We found that the average density of elements on Chromosome 10 is 22.321/Mb (Table 3). There is a nonrandom clustering of both copia-like and gypsy-like LTR retrotransposons along the chromosome (Figure 6, 7 and 8).

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