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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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Four cases of association between retroelements with O. sativa putative genes observed in this study. Red arrows indicate positions of LTR retroelements with the direction of transcription. Green bars represent NCBI database-predicted gene regions with their orientation of transcription. All the four associations (from F to I) are located in the following genomic clones: AP003627, AC079685, AP003021 and AP003144. (F) An Osr34 solo LTR is associated with two putative genes nearby (P0459B04.22 and P0459B04.23) of unknown function. (G) An Osr8 fragmented LTR is partly associated with a putative LeoOPT1 (oligopeptide transport) gene (OSJNBb0012A20.5). (H) An Osr13 solo LTR constitutes almost half of a putative gene (P0503E05.17) of unknown function; (I) An Osr13 full-length retrotransposon is part of a putative rice gene (P0507H05.22) of unknown function.
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Figure 10: Four cases of association between retroelements with O. sativa putative genes observed in this study. Red arrows indicate positions of LTR retroelements with the direction of transcription. Green bars represent NCBI database-predicted gene regions with their orientation of transcription. All the four associations (from F to I) are located in the following genomic clones: AP003627, AC079685, AP003021 and AP003144. (F) An Osr34 solo LTR is associated with two putative genes nearby (P0459B04.22 and P0459B04.23) of unknown function. (G) An Osr8 fragmented LTR is partly associated with a putative LeoOPT1 (oligopeptide transport) gene (OSJNBb0012A20.5). (H) An Osr13 solo LTR constitutes almost half of a putative gene (P0503E05.17) of unknown function; (I) An Osr13 full-length retrotransposon is part of a putative rice gene (P0507H05.22) of unknown function.

Mentions: In an initial effort to determine whether and how frequently LTR retrotransposon sequences are associated with putative genes in the rice genome, we examined elements from all 19 families of copia-like elements and 5 representative families gypsy-like elements present in O. sativa. Our results indicate that 111/510 or 22% of LTR retrotransposon sequences lie within putative or established rice genes over the region of the genome analyzed in this study (Table 4, Figure 9 and 10). Fragmented elements are more frequently associated with genes (16%), followed by solo LTRs (3%) and full-length elements (2%). While these numbers are likely to change somewhat as the rice genome is better annotated, these preliminary estimates indicate that the potential contribution of LTR retrotranspson sequences to the evolution of gene structure and function in rice may be significant.


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)

Four cases of association between retroelements with O. sativa putative genes observed in this study. Red arrows indicate positions of LTR retroelements with the direction of transcription. Green bars represent NCBI database-predicted gene regions with their orientation of transcription. All the four associations (from F to I) are located in the following genomic clones: AP003627, AC079685, AP003021 and AP003144. (F) An Osr34 solo LTR is associated with two putative genes nearby (P0459B04.22 and P0459B04.23) of unknown function. (G) An Osr8 fragmented LTR is partly associated with a putative LeoOPT1 (oligopeptide transport) gene (OSJNBb0012A20.5). (H) An Osr13 solo LTR constitutes almost half of a putative gene (P0503E05.17) of unknown function; (I) An Osr13 full-length retrotransposon is part of a putative rice gene (P0507H05.22) of unknown function.
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Related In: Results  -  Collection

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Figure 10: Four cases of association between retroelements with O. sativa putative genes observed in this study. Red arrows indicate positions of LTR retroelements with the direction of transcription. Green bars represent NCBI database-predicted gene regions with their orientation of transcription. All the four associations (from F to I) are located in the following genomic clones: AP003627, AC079685, AP003021 and AP003144. (F) An Osr34 solo LTR is associated with two putative genes nearby (P0459B04.22 and P0459B04.23) of unknown function. (G) An Osr8 fragmented LTR is partly associated with a putative LeoOPT1 (oligopeptide transport) gene (OSJNBb0012A20.5). (H) An Osr13 solo LTR constitutes almost half of a putative gene (P0503E05.17) of unknown function; (I) An Osr13 full-length retrotransposon is part of a putative rice gene (P0507H05.22) of unknown function.
Mentions: In an initial effort to determine whether and how frequently LTR retrotransposon sequences are associated with putative genes in the rice genome, we examined elements from all 19 families of copia-like elements and 5 representative families gypsy-like elements present in O. sativa. Our results indicate that 111/510 or 22% of LTR retrotransposon sequences lie within putative or established rice genes over the region of the genome analyzed in this study (Table 4, Figure 9 and 10). Fragmented elements are more frequently associated with genes (16%), followed by solo LTRs (3%) and full-length elements (2%). While these numbers are likely to change somewhat as the rice genome is better annotated, these preliminary estimates indicate that the potential contribution of LTR retrotranspson sequences to the evolution of gene structure and function in rice may be significant.

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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