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Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Author

Listed:
  • Xueyan Li

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Dingding Fan

    (BGI-Shenzhen)

  • Wei Zhang

    (University of Chicago)

  • Guichun Liu

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Lu Zhang

    (BGI-Shenzhen
    City University of Hongkong)

  • Li Zhao

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
    University of California Davis, Davis, California 95616, USA)

  • Xiaodong Fang

    (BGI-Shenzhen)

  • Lei Chen

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yang Dong

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
    Present address: College of Life Science, Kunming University of Science and Technology, Kunming 650093, China)

  • Yuan Chen

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
    Present address: Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA)

  • Yun Ding

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
    Present address: Janelia Research Campus, Howard Hughes Medical Institute, Ashbum, VA 20147, USA)

  • Ruoping Zhao

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Mingji Feng

    (BGI-Shenzhen)

  • Yabing Zhu

    (BGI-Shenzhen)

  • Yue Feng

    (BGI-Shenzhen)

  • Xuanting Jiang

    (BGI-Shenzhen)

  • Deying Zhu

    (BGI-Shenzhen
    School of Bioscience and Biotechnology, South China University of Technology)

  • Hui Xiang

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

  • Xikan Feng

    (BGI-Shenzhen
    City University of Hongkong)

  • Shuaicheng Li

    (City University of Hongkong)

  • Jun Wang

    (BGI-Shenzhen)

  • Guojie Zhang

    (BGI-Shenzhen
    Centre for Social Evolution, Universitetsparken 15, University of Copenhagen)

  • Marcus R. Kronforst

    (University of Chicago)

  • Wen Wang

    (State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences)

Abstract

Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system.

Suggested Citation

  • Xueyan Li & Dingding Fan & Wei Zhang & Guichun Liu & Lu Zhang & Li Zhao & Xiaodong Fang & Lei Chen & Yang Dong & Yuan Chen & Yun Ding & Ruoping Zhao & Mingji Feng & Yabing Zhu & Yue Feng & Xuanting Ji, 2015. "Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies," Nature Communications, Nature, vol. 6(1), pages 1-10, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9212
    DOI: 10.1038/ncomms9212
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    Cited by:

    1. Balázs Bálint & Zsolt Merényi & Botond Hegedüs & Igor V. Grigoriev & Zhihao Hou & Csenge Földi & László G. Nagy, 2024. "ContScout: sensitive detection and removal of contamination from annotated genomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Botong Zhou & Ping Hu & Guichun Liu & Zhou Chang & Zhiwei Dong & Zihe Li & Yuan Yin & Zunzhe Tian & Ge Han & Wen Wang & Xueyan Li, 2024. "Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Youjie Zhao & Chengyong Su & Bo He & Ruie Nie & Yunliang Wang & Junye Ma & Jingyu Song & Qun Yang & Jiasheng Hao, 2023. "Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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