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Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber

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  • Hongbo Li

    (Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
    Qingdao Agricultural University
    Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences)

  • Shenhao Wang

    (Northwest A&F University)

  • Sen Chai

    (Qingdao Agricultural University)

  • Zhiquan Yang

    (Huazhong Agricultural University)

  • Qiqi Zhang

    (Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences)

  • Hongjia Xin

    (Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences)

  • Yuanchao Xu

    (Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences)

  • Shengnan Lin

    (Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
    Huazhong Agricultural University)

  • Xinxiu Chen

    (Qingdao Agricultural University)

  • Zhiwang Yao

    (Qingdao Agricultural University)

  • Qingyong Yang

    (Huazhong Agricultural University)

  • Zhangjun Fei

    (Cornell University
    Robert W. Holley Center for Agriculture and Health)

  • Sanwen Huang

    (Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences)

  • Zhonghua Zhang

    (Qingdao Agricultural University)

Abstract

Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.

Suggested Citation

  • Hongbo Li & Shenhao Wang & Sen Chai & Zhiquan Yang & Qiqi Zhang & Hongjia Xin & Yuanchao Xu & Shengnan Lin & Xinxiu Chen & Zhiwang Yao & Qingyong Yang & Zhangjun Fei & Sanwen Huang & Zhonghua Zhang, 2022. "Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28362-0
    DOI: 10.1038/s41467-022-28362-0
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    1. Daiqi Wang & Hongru Wang & Xiaomei Xu & Man Wang & Yahuan Wang & Hong Chen & Fei Ping & Huanhuan Zhong & Zhengkun Mu & Wantong Xie & Xiangyu Li & Jingbin Feng & Milan Zhang & Zhilan Fan & Tifeng Yang , 2023. "Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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