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Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences.
BMC Genomics. 2004 Mar 02; 5(1):18.BG

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.

Authors+Show Affiliations

Department of Genetics, University of Georgia, Athens, Georgia 30602, USA. LZGao@sph.uth.tmc.eduNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

15040813

Citation

Gao, Lizhi, et al. "Evolutionary History of Oryza Sativa LTR Retrotransposons: a Preliminary Survey of the Rice Genome Sequences." BMC Genomics, vol. 5, no. 1, 2004, p. 18.
Gao L, McCarthy EM, Ganko EW, et al. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics. 2004;5(1):18.
Gao, L., McCarthy, E. M., Ganko, E. W., & McDonald, J. F. (2004). Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics, 5(1), 18.
Gao L, et al. Evolutionary History of Oryza Sativa LTR Retrotransposons: a Preliminary Survey of the Rice Genome Sequences. BMC Genomics. 2004 Mar 2;5(1):18. PubMed PMID: 15040813.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. AU - Gao,Lizhi, AU - McCarthy,Eugene M, AU - Ganko,Eric W, AU - McDonald,John F, Y1 - 2004/03/02/ PY - 2003/09/16/received PY - 2004/03/02/accepted PY - 2004/3/26/pubmed PY - 2004/12/16/medline PY - 2004/3/26/entrez SP - 18 EP - 18 JF - BMC genomics JO - BMC Genomics VL - 5 IS - 1 N2 - 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/15040813/Evolutionary_history_of_Oryza_sativa_LTR_retrotransposons:_a_preliminary_survey_of_the_rice_genome_sequences_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-5-18 DB - PRIME DP - Unbound Medicine ER -