A syntelog-based pan-genome provides insights into rice domestication and de-domestication

文献类型： 外文期刊

第一作者： Wu, Dongya

作者： Wu, Dongya;Shen, Enhui;Fan, Longjiang;Wu, Dongya;Xie, Lingjuan;Sun, Yanqing;Huang, Yujie;Jia, Lei;Dong, Chenfeng;Shen, Enhui;Ye, Chu-Yu;Fan, Longjiang;Wu, Dongya;Huang, Yujie;Qian, Qian

作者机构：

关键词： Rice pan-genome; Syntelog; Domestication; De-domestication; Introgression

期刊名称：GENOME BIOLOGY （ 影响因子：12.3； 五年影响因子：17.4 ）

ISSN： 1474-760X

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundAsian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate.ResultsHere, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice.ConclusionsThis work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.

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