A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation

文献类型： 外文期刊

第一作者： Hu, Guanjing

作者： Hu, Guanjing;Wang, Zhenyu;Ji, Gaoxiang;Wang, Xingxing;Zhang, Xianliang;Yang, Zhaoen;Niu, Ruoyu;Zhang, Yuzhi;Duan, Lian;Zhao, Junjie;He, Shoupu;Zang, Xinshan;Ma, Xiongfeng;Hu, Guanjing;Tian, Zunzhe;Liu, Xuan;Niu, Ruoyu;Zhu, De;Duan, Lian;Ma, Xueyuan;Xiong, Xianpeng;Kong, Jiali;Zhao, Xianjia;Zhang, Ya;Wu, Zhiqiang;Pan, Weihua;Ma, Xiongfeng;Wang, Zhenyu;Ji, Gaoxiang;Wang, Xingxing;Zhang, Xianliang;Yang, Zhaoen;Liu, Xuan;Zhao, Junjie;He, Shoupu;Zang, Xinshan;Ma, Xiongfeng;Wang, Kai;Yu, Guangrun;Han, Jinlei;Zhang, Xianliang;Grover, Corrinne E.;Wendel, Jonathan F.;Su, Junji;Feng, Keyun

作者机构：

期刊名称：NATURE GENETICS （ 影响因子：29.0； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2025 年 57 卷 4 期

页码：

收录情况： SCI

摘要： Cotton (Gossypium hirsutum L.) is a key allopolyploid crop with global economic importance. Here we present a telomere-to-telomere assembly of the elite variety Zhongmian 113. Leveraging technologies including PacBio HiFi, Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C, our assembly surpasses previous genomes in contiguity and completeness, resolving 26 centromeric and 52 telomeric regions, 5S rDNA clusters and nucleolar organizer regions. A phylogenetically recent centromere repositioning on chromosome D08 was discovered specific to G. hirsutum, involving deactivation of an ancestral centromere and the formation of a unique, satellite repeat-based centromere. Genomic analyses evaluated favorable allele aggregation for key agronomic traits and uncovered an early-maturing haplotype derived from an 11 Mb pericentric inversion that evolved early during G. hirsutum domestication. Our study sheds light on the genomic origins of short-season adaptation, potentially involving introgression of an inversion from primitively domesticated forms, followed by subsequent haplotype differentiation in modern breeding programs.

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