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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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Phylogenetic trees of subfamily structure based on LTR nucleotide sequence data. The Osr27 family forms at least 10 divergent clades with strong bootstrap support, with Osr41 as the outgroup. To better exhibit tree structure, all Osr27 elements were removed. Insertions/deletions were ignored while performing phylogenetic analyses. Values on individual branches are bootstrap percentages using 1000 bootstrap repetitions. Each LTR in the tree is named by the genomic clone in which it was found. For elements with two LTRs, the 3' LTR is labeled by a lower case "b" while the 5' LTR is labeled by a lower case "a". Each tree is exhibited with a scale bar determined by the number of nucleotide substitutions per site between two sequences. The tight clustering seen in both families represents a high degree of nucleotide identity between elements within a subfamily.
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Figure 2: Phylogenetic trees of subfamily structure based on LTR nucleotide sequence data. The Osr27 family forms at least 10 divergent clades with strong bootstrap support, with Osr41 as the outgroup. To better exhibit tree structure, all Osr27 elements were removed. Insertions/deletions were ignored while performing phylogenetic analyses. Values on individual branches are bootstrap percentages using 1000 bootstrap repetitions. Each LTR in the tree is named by the genomic clone in which it was found. For elements with two LTRs, the 3' LTR is labeled by a lower case "b" while the 5' LTR is labeled by a lower case "a". Each tree is exhibited with a scale bar determined by the number of nucleotide substitutions per site between two sequences. The tight clustering seen in both families represents a high degree of nucleotide identity between elements within a subfamily.

Mentions: The Osr26 family, for example, is comprised of 32 elements falling into at least 5 distinct clades (Fig. 1). The Osr27 family, which is composed of 134 elements, displayed complicated substructure, consisting of at least 10 divergent clades with strong bootstrap support (Fig. 2). The remaining 27 families are closely related and displayed no significant intra-family substructure.


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)

Phylogenetic trees of subfamily structure based on LTR nucleotide sequence data. The Osr27 family forms at least 10 divergent clades with strong bootstrap support, with Osr41 as the outgroup. To better exhibit tree structure, all Osr27 elements were removed. Insertions/deletions were ignored while performing phylogenetic analyses. Values on individual branches are bootstrap percentages using 1000 bootstrap repetitions. Each LTR in the tree is named by the genomic clone in which it was found. For elements with two LTRs, the 3' LTR is labeled by a lower case "b" while the 5' LTR is labeled by a lower case "a". Each tree is exhibited with a scale bar determined by the number of nucleotide substitutions per site between two sequences. The tight clustering seen in both families represents a high degree of nucleotide identity between elements within a subfamily.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Phylogenetic trees of subfamily structure based on LTR nucleotide sequence data. The Osr27 family forms at least 10 divergent clades with strong bootstrap support, with Osr41 as the outgroup. To better exhibit tree structure, all Osr27 elements were removed. Insertions/deletions were ignored while performing phylogenetic analyses. Values on individual branches are bootstrap percentages using 1000 bootstrap repetitions. Each LTR in the tree is named by the genomic clone in which it was found. For elements with two LTRs, the 3' LTR is labeled by a lower case "b" while the 5' LTR is labeled by a lower case "a". Each tree is exhibited with a scale bar determined by the number of nucleotide substitutions per site between two sequences. The tight clustering seen in both families represents a high degree of nucleotide identity between elements within a subfamily.
Mentions: The Osr26 family, for example, is comprised of 32 elements falling into at least 5 distinct clades (Fig. 1). The Osr27 family, which is composed of 134 elements, displayed complicated substructure, consisting of at least 10 divergent clades with strong bootstrap support (Fig. 2). The remaining 27 families are closely related and displayed no significant intra-family substructure.

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