A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

文献类型： 外文期刊

第一作者： Zhang, Anqi

作者： Zhang, Anqi;Kong, Tangchao;Qiu, Shizheng;Guo, Jiahe;Ruan, Shuyong;Guo, Yu;Guo, Jirui;Zhang, Zhishuai;Liu, Yue;Hu, Zheng;Jiang, Tao;Liu, Yadong;Cao, Shuqi;Hu, Yang;Liu, Bo;Wang, Yadong;Sun, Baiquan;Sun, Shi;Wu, Tingting;Jiang, Bingjun;Yang, Maoxiang;Yao, Xiangyu;Han, Tianfu;Hong, Huilong

作者机构：

关键词： Soybean; Telomere-to-Telomere assembly; Zhonghuang 13; Structure variations

期刊名称：CROP JOURNAL （ 影响因子：6.6； 五年影响因子：6.5 ）

ISSN： 2095-5421

年卷期： 2024 年 12 卷 1 期

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收录情况： SCI

摘要： Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar Zhonghuang 13 (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution. (c) 2023 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NCND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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