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Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

Author

Listed:
  • Sebastian Reyes-Chin-Wo

    (UC Davis Genome Center)

  • Zhiwen Wang

    (BGI Shenzhen
    Present address: PubBio-Tech, Wuhan 430070, China)

  • Xinhua Yang

    (BGI Shenzhen)

  • Alexander Kozik

    (UC Davis Genome Center)

  • Siwaret Arikit

    (Delaware Biotechnology Institute, University of Delaware
    Present address: Rice Science Center, and Department of Agronomy, Faculty of Agriculture, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand)

  • Chi Song

    (BGI Shenzhen)

  • Liangfeng Xia

    (BGI Shenzhen)

  • Lutz Froenicke

    (UC Davis Genome Center)

  • Dean O. Lavelle

    (UC Davis Genome Center)

  • María-José Truco

    (UC Davis Genome Center)

  • Rui Xia

    (Donald Danforth Plant Science Center)

  • Shilin Zhu

    (BGI Shenzhen)

  • Chunyan Xu

    (BGI Shenzhen)

  • Huaqin Xu

    (UC Davis Genome Center)

  • Xun Xu

    (BGI Shenzhen)

  • Kyle Cox

    (UC Davis Genome Center)

  • Ian Korf

    (UC Davis Genome Center
    Department of Molecular & Cellular Biology)

  • Blake C. Meyers

    (Delaware Biotechnology Institute, University of Delaware
    Donald Danforth Plant Science Center)

  • Richard W. Michelmore

    (UC Davis Genome Center
    Department of Molecular & Cellular Biology
    Department of Plant Sciences
    Department of Medical Microbiology & Immunology)

Abstract

Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.

Suggested Citation

  • Sebastian Reyes-Chin-Wo & Zhiwen Wang & Xinhua Yang & Alexander Kozik & Siwaret Arikit & Chi Song & Liangfeng Xia & Lutz Froenicke & Dean O. Lavelle & María-José Truco & Rui Xia & Shilin Zhu & Chunyan, 2017. "Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14953
    DOI: 10.1038/ncomms14953
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    Cited by:

    1. Zhen-Hui Wang & Xin-Feng Wang & Tianyuan Lu & Ming-Rui Li & Peng Jiang & Jing Zhao & Si-Tong Liu & Xue-Qi Fu & Jonathan F. Wendel & Yves Peer & Bao Liu & Lin-Feng Li, 2022. "Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Fei Shen & Yajuan Qin & Rui Wang & Xin Huang & Ying Wang & Tiangang Gao & Junna He & Yue Zhou & Yuannian Jiao & Jianhua Wei & Lei Li & Xiaozeng Yang, 2023. "Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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