A super pan-genomic landscape of rice

文献类型： 外文期刊

第一作者： Shang, Lianguang

作者： Shang, Lianguang;Li, Xiaoxia;He, Huiying;Yuan, Qiaoling;Song, Yanni;Wei, Zhaoran;Lin, Hai;Zhao, Fengli;Zhang, Chao;Li, Yuhua;Gao, Hongsheng;Wang, Tianyi;Liu, Xiangpei;Zhang, Hong;Zhang, Ya;Cao, Shuaimin;Yu, Xiaoman;Zhang, Bintao;Zhang, Yong;Qin, Mao;Ai, Cheng;Yang, Yingxue;Zhang, Bin;Lv, Yang;Wang, Quan;Zhou, Yongfeng;Ruan, Jue;Qian, Qian;Hu, Min;Zhu, Zuofeng;Tan, Yiqing;Xiong, Guosheng;Hu, Zhiqiang;Wang, Hongru;Lv, Yang;Wang, Yuexing;Ma, Jie;Guo, Longbiao;Qian, Qian;Lu, Hongwei;Wu, Zhe;Liu, Shanlin;Sun, Zongyi;Zhang, Hongliang;Li, Zichao;Li, Jiayang

作者机构：

期刊名称：CELL RESEARCH （ 影响因子：46.297； 五年影响因子：38.109 ）

ISSN： 1001-0602

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收录情况： SCI

摘要： Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

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