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A Super Pan-Genomic Landscape of Rice

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