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Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species.
G3 (Bethesda). 2017 06 07; 7(6):1875-1885.G

Abstract

The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice.

Authors+Show Affiliations

Plant Germplasm and Genomics Center, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204 China. University of the Chinese Academy of Sciences, Beijing 100039, China. Agrobiological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.Plant Germplasm and Genomics Center, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204 China lgao@mail.kib.ac.cn.

Pub Type(s)

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

Language

eng

PubMed ID

28413161

Citation

Zhang, Qun-Jie, and Li-Zhi Gao. "Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species." G3 (Bethesda, Md.), vol. 7, no. 6, 2017, pp. 1875-1885.
Zhang QJ, Gao LZ. Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. G3 (Bethesda). 2017;7(6):1875-1885.
Zhang, Q. J., & Gao, L. Z. (2017). Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. G3 (Bethesda, Md.), 7(6), 1875-1885. https://doi.org/10.1534/g3.116.037572
Zhang QJ, Gao LZ. Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. G3 (Bethesda). 2017 06 7;7(6):1875-1885. PubMed PMID: 28413161.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. AU - Zhang,Qun-Jie, AU - Gao,Li-Zhi, Y1 - 2017/06/07/ PY - 2017/4/18/pubmed PY - 2018/3/27/medline PY - 2017/4/18/entrez KW - AA-genome KW - LTR retrotransposons KW - Oryza KW - comparative genomics KW - rice speciation SP - 1875 EP - 1885 JF - G3 (Bethesda, Md.) JO - G3 (Bethesda) VL - 7 IS - 6 N2 - The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice. SN - 2160-1836 UR - https://www.unboundmedicine.com/medline/citation/28413161/Rapid_and_Recent_Evolution_of_LTR_Retrotransposons_Drives_Rice_Genome_Evolution_During_the_Speciation_of_AA_Genome_Oryza_Species_ L2 - http://www.g3journal.org/cgi/pmidlookup?view=long&pmid=28413161 DB - PRIME DP - Unbound Medicine ER -