数字农科院2.0

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

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

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关键词： （1-1-2）

期刊名称： NATURE GENETICS

ISSN： 1061-4036

年卷期： 2025 年

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收录情况： SCIE（2025版）

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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