Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species

文献类型： 外文期刊

第一作者： Zhang, Qun-Jie

作者： Zhang, Qun-Jie;Gao, Li-Zhi;Zhang, Qun-Jie;Zhang, Qun-Jie

作者机构：

关键词： LTR retrotransposons;Oryza;AA-genome;rice speciation;comparative genomics

期刊名称：G3-GENES GENOMES GENETICS （ 影响因子：3.154； 五年影响因子：3.369 ）

ISSN： 2160-1836

年卷期： 2017 年 7 卷 6 期

页码：

收录情况： SCI

摘要： 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 similar to 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.

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