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

doi:10.1534/g3.116.037572

	Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species
	Zhang, Qun-Jie 1,2,3; Gao, Li-Zhi1
	2017-06-01
发表期刊	G3-GENES GENOMES GENETICS
卷号	7 页码:1875-1885
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.
关键词	Ltr Retrotransposons Oryza Aa-genome Rice Speciation Comparative Genomics
DOI	10.1534/g3.116.037572
收录类别	SCI
语种	英语
WOS记录号	WOS:000403075000024
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/51361
专题	中国西南野生生物种质资源库
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Kunming 650204, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China 3.Guangdong Acad Agr Sci, Agrobiol Gene Res Ctr, Guangzhou 510640, Guangdong, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Qun-Jie,Gao, Li-Zhi. Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species[J]. G3-GENES GENOMES GENETICS,2017,7:1875-1885.
APA	Zhang, Qun-Jie,&Gao, Li-Zhi.(2017).Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species.G3-GENES GENOMES GENETICS,7,1875-1885.
MLA	Zhang, Qun-Jie,et al."Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species".G3-GENES GENOMES GENETICS 7(2017):1875-1885.

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
086041.full.pdf（2083KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览下载