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

作　　者：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 

机构地区：[1]Center for Bioinformatics,School of Computer Science and Technology,Harbin Institute of Technology,Harbin 150001,Heilongjiang,China [2]Ministry of Agriculture Key Laboratory of Soybean Biology(Beijing),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China [3]National Key Facility for Crop Gene Resources and Genetic Improvement,Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China

出　　处：《The Crop Journal》2024年第1期142-153,共12页作物学报（英文版）

基　　金：This work has been supported by the National Key Research and Development Program of China(2021YFF1200105);National Natural Science Foundation of China(62172125,62371161).

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.

关 键 词：SOYBEAN Telomere-to-Telomere assembly Zhonghuang 13 Structure variations 

分 类 号：S565.1[农业科学—作物学]