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

• DOI: 10.1016/j.cj.2023.10.003
• Publication Date: 2023-11-03T20:15:02Z
• Authors: 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
• Keywords: 2. Zero hunger; 0303 health sciences; 03 medical and health sciences; S; Agriculture (General); Structure variations; Zhonghuang 13; Agriculture; Soybean; Telomere-to-Telomere assembly; S1-972

AbstractSoybean (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 the first 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.