IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-28362-0.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-28362-0
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-28362-0?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Rico Gamuyao & Joong Hyoun Chin & Juan Pariasca-Tanaka & Paolo Pesaresi & Sheryl Catausan & Cheryl Dalid & Inez Slamet-Loedin & Evelyn Mae Tecson-Mendoza & Matthias Wissuwa & Sigrid Heuer, 2012. "The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency," Nature, Nature, vol. 488(7412), pages 535-539, August.
    2. Kenong Xu & Xia Xu & Takeshi Fukao & Patrick Canlas & Reycel Maghirang-Rodriguez & Sigrid Heuer & Abdelbagi M. Ismail & Julia Bailey-Serres & Pamela C. Ronald & David J. Mackill, 2006. "Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice," Nature, Nature, vol. 442(7103), pages 705-708, August.
    3. Dasen Xie & Yuanchao Xu & Jinpeng Wang & Wenrui Liu & Qian Zhou & Shaobo Luo & Wu Huang & Xiaoming He & Qing Li & Qingwu Peng & Xueyong Yang & Jiaqing Yuan & Jigao Yu & Xiyin Wang & William J. Lucas &, 2019. "The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    4. Daniel C. Jeffares & Clemency Jolly & Mimoza Hoti & Doug Speed & Liam Shaw & Charalampos Rallis & Francois Balloux & Christophe Dessimoz & Jürg Bähler & Fritz J. Sedlazeck, 2017. "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    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.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    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.
    2. Abdul Rehman & Luan Jingdong & Abbas Ali Chandio & Muhammad Shabbir & Imran Hussain, 2017. "Economic outlook of rice crops in Pakistan: a time series analysis (1970–2015)," Financial Innovation, Springer;Southwestern University of Finance and Economics, vol. 3(1), pages 1-9, December.
    3. Hifzur RAHMAN & Vijayalakshmi DAKSHINAMURTHI & Sasikala RAMASAMY & Sudha MANICKAM & Ashok Kumar KALIYAPERUMAL & Suchismita RAHA & Naresh PANNEERSELVAM & Valarmathi RAMANATHAN & Jagadeeshselvam NALLATH, 2018. "Introgression of submergence tolerance into CO 43, a popular rice variety of India, through marker-assisted backcross breeding," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 54(3), pages 101-108.
    4. Liyuan Zhou & Qiongzi Qiu & Qing Zhou & Jianwei Li & Mengqian Yu & Kezhen Li & Lingling Xu & Xiaohui Ke & Haiming Xu & Bingjian Lu & Hui Wang & Weiguo Lu & Pengyuan Liu & Yan Lu, 2022. "Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Mariola Staniak & Ewa Szpunar-Krok & Anna Kocira, 2023. "Responses of Soybean to Selected Abiotic Stresses—Photoperiod, Temperature and Water," Agriculture, MDPI, vol. 13(1), pages 1-28, January.
    6. Jinhyun Kim & Sungsik Kim & Huiran Yeom & Seo Woo Song & Kyoungseob Shin & Sangwook Bae & Han Suk Ryu & Ji Young Kim & Ahyoun Choi & Sumin Lee & Taehoon Ryu & Yeongjae Choi & Hamin Kim & Okju Kim & Yu, 2023. "Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    7. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    8. Yingyan Yu & Zhen Zhang & Xiaorui Dong & Ruixin Yang & Zhongqu Duan & Zhen Xiang & Jun Li & Guichao Li & Fazhe Yan & Hongzhang Xue & Du Jiao & Jinyuan Lu & Huimin Lu & Wenmin Zhang & Yangzhen Wei & Sh, 2022. "Pangenomic analysis of Chinese gastric cancer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    9. Mei Chen & Xin Luo & Long Jiang & Rui Dong & K.H.M. Siddique & Jin He, 2023. "Legume crops use a phosphorus-mobilising strategy to adapt to low plant-available phosphorus in acidic soil in southwest China," Plant, Soil and Environment, Czech Academy of Agricultural Sciences, vol. 69(10), pages 471-479.
    10. Kyle Emerick & Alain de Janvry & Elisabeth Sadoulet & Manzoor H. Dar, 2016. "Technological Innovations, Downside Risk, and the Modernization of Agriculture," American Economic Review, American Economic Association, vol. 106(6), pages 1537-1561, June.
    11. Emerick, Kyle, 2018. "Trading frictions in Indian village economies," Journal of Development Economics, Elsevier, vol. 132(C), pages 32-56.
    12. Laxmi Prasad Pant, 2019. "Responsible innovation through conscious contestation at the interface of agricultural science, policy, and civil society," Agriculture and Human Values, Springer;The Agriculture, Food, & Human Values Society (AFHVS), vol. 36(2), pages 183-197, June.
    13. Xuelin Xie & Jingfang Shen, 2021. "Waterlogging Resistance Evaluation Index and Photosynthesis Characteristics Selection: Using Machine Learning Methods to Judge Poplar’s Waterlogging Resistance," Mathematics, MDPI, vol. 9(13), pages 1-19, July.
    14. Isnaini Isnaini & Yudhistira Nugraha & Niranjan Baisakh & Nono Carsono, 2023. "Toward Food Security in 2050: Gene Pyramiding for Climate-Smart Rice," Sustainability, MDPI, vol. 15(19), pages 1-35, September.
    15. Naser Ansari-Pour & Yonglan Zheng & Toshio F. Yoshimatsu & Ayodele Sanni & Mustapha Ajani & Jean-Baptiste Reynier & Avraam Tapinos & Jason J. Pitt & Stefan Dentro & Anna Woodard & Padma Sheila Rajagop, 2021. "Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    16. Jian Sun & Guangchen Zhang & Zhibo Cui & Ximan Kong & Xiaoyu Yu & Rui Gui & Yuqing Han & Zhuan Li & Hong Lang & Yuchen Hua & Xuemin Zhang & Quan Xu & Liang Tang & Zhengjin Xu & Dianrong Ma & Wenfu Che, 2022. "Regain flood adaptation in rice through a 14-3-3 protein OsGF14h," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    17. Goutam Das & Banshidhar Pradhan & Debendranath Bastia & Sanghamitra Samantaray & Debarchana Jena & Diptibala Rout & Paduranga Bhagwan Arsode & Vineeta Singh & Arup Kumar Mukherjee & Chander Mohan & Ra, 2022. "Pyramiding Submergence Tolerance and Three Bacterial Blight Resistance Genes in Popular Rice Variety Hasanta through Marker-Assisted Backcross Breeding," Agriculture, MDPI, vol. 12(11), pages 1-26, October.
    18. Agata Zubrycka & Charlene Dambire & Laura Dalle Carbonare & Gunjan Sharma & Tinne Boeckx & Kamal Swarup & Craig J. Sturrock & Brian S. Atkinson & Ranjan Swarup & Françoise Corbineau & Neil J. Oldham &, 2023. "ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    19. Zilong Guo & Hongrui Cao & Jing Zhao & Shuang Bai & Wenting Peng & Jian Li & Lili Sun & Liyu Chen & Zhihao Lin & Chen Shi & Qing Yang & Yongqing Yang & Xiurong Wang & Jiang Tian & Zhichang Chen & Hong, 2022. "A natural uORF variant confers phosphorus acquisition diversity in soybean," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    20. Michalak Dorota & Wulf Erico, 2019. "Priority Areas of Poland’s Development in Line with EU Policy (Smart Specializations) – Poland’s Food Security and Climate Change," Journal of Intercultural Management, Sciendo, vol. 11(4), pages 158-182, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28362-0. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.