A reference-grade wild soybean genome

Research output: Contribution to journalArticlepeer-review


  • Min Xie
  • Claire Yik Lok Chung
  • Man Wah Li
  • Fuk Ling Wong
  • Xin Wang
  • Ailin Liu
  • Zhili Wang
  • Alden King Yung Leung
  • Tin Hang Wong
  • Suk Wah Tong
  • Zhixia Xiao
  • Kejing Fan
  • Ming Sin Ng
  • Xinpeng Qi
  • Linfeng Yang
  • Tianquan Deng
  • Lijuan He
  • Lu Chen
  • Aisi Fu
  • Qiong Ding
  • Junxian He
  • Gyuhwa Chung
  • Sachiko Isobe
  • Takanari Tanabata
  • Babu Valliyodan
  • Henry T. Nguyen
  • Steven B. Cannon
  • Ting Fung Chan
  • Hon Ming Lam

Colleges, School and Institutes

External organisations

  • The Chinese University of Hong Kong
  • BGI-Shenzhen
  • Wuhan Institute of Biotechnology
  • Chonnam National University
  • Kazusa DNA Research Institute
  • University of Missouri-Columbia
  • United States Department of Agriculture
  • Faculty of Biological Sciences
  • University of Leeds


Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.


Original languageEnglish
Article number1216
Number of pages12
JournalNature Communications
Issue number1
Publication statusPublished - 14 Mar 2019