A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max
Anqi Zhang,
Tangchao Kong,
Baiquan Sun,
Shizheng Qiu,
Jiahe Guo,
Shuyong Ruan,
Yu Guo,
Jirui Guo,
Zhishuai Zhang,
Yue Liu,
Zheng Hu,
Tao Jiang,
Yadong Liu,
Shuqi Cao,
Shi Sun,
Tingting Wu,
Huilong Hong,
Bingjun Jiang,
Maoxiang Yang,
Xiangyu Yao,
Yang Hu,
Bo Liu,
Tianfu Han,
Yadong Wang
Affiliations
Anqi Zhang
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Tangchao Kong
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Baiquan Sun
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Shizheng Qiu
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Jiahe Guo
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Shuyong Ruan
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Yu Guo
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Jirui Guo
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Zhishuai Zhang
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Yue Liu
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Zheng Hu
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Tao Jiang
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Yadong Liu
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Shuqi Cao
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China
Shi Sun
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Tingting Wu
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Huilong Hong
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Bingjun Jiang
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Maoxiang Yang
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Xiangyu Yao
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Yang Hu
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; Corresponding authors.
Bo Liu
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; Corresponding authors.
Tianfu Han
Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Corresponding authors.
Yadong Wang
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, Heilongjiang, China; Corresponding authors.
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.
