Gapless pangenome analyses reveal fast Brassica rapa subspeciation

• 成果类型: Article
• 署名作者: Ma, Wei; Liu, Yuanming; Wei, Xiaochun; Zhang, Xiaomeng; Li, Xiaonan; Liu, Zhaokun; Yuan, Lingyun; Li, Guangguang; Zhang, Shu; Yang, Qihang; Chang, Xiaocong; Han, Zizhuo; Liang, Hao; Luan, Zhaoshui; Wang, Qianyun; Gu, Yujie; Wang, Xinlong; Zhao, Xianlei; Liu, Qing; Sun, Xiaoxue; Liu, Mengyang; Feng, Daling; Lu, Yin; Luo, Shuangxia; Yang, Lei; Li, Mengyuan; Allaby, Robin; Wang, Kai; Zhang, Tianzhen; Shen, Shuxing; Van De Peer, Yves; Hong, Yiguo; Yuan, Yuxiang; Zhao, Jianjun
• 署名单位: Hebei Agricultural University; Henan Academy of Agricultural Sciences; Shenyang Agricultural University; Jiangsu Academy of Agricultural Sciences; Anhui Agricultural University; University of Warwick; Nantong University; Zhejiang University; Ghent University; Flanders Institute for Biotechnology (VIB); Ghent University; University of Pretoria; Nanjing Agricultural University
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-8075; 1095-9203
• DOI: 10.1126/science.ady7590
• 发表日期: 2026-02-05
• 页码: eady7590
• 关键词: genome; centromere; domestication; expression; GROWTH; retrotransposons; diversification; interacts; sequence; pollen

摘要

Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with Br morphotypes and subspecies and Brassica species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among Br subspecies. Pangenome-wide association studies uncovered that the gene BrLH1 controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of Br cultivation, providing invaluable resources for Brassica breeding.