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Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes

Author

Listed:
  • Hangxing Jia

    (Chinese Academy of Sciences)

  • Shengjun Tan

    (Chinese Academy of Sciences)

  • Yingao Cai

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yanyan Guo

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jieyu Shen

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yaqiong Zhang

    (Chinese Academy of Sciences)

  • Huijing Ma

    (Chinese Academy of Sciences)

  • Qingzhu Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jinfeng Chen

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Gexia Qiao

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jue Ruan

    (Chinese Academy of Agricultural Sciences)

  • Yong E. Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

Abstract

Long-read sequencing, exemplified by PacBio, revolutionizes genomics, overcoming challenges like repetitive sequences. However, the high DNA requirement ( > 1 µg) is prohibitive for small organisms. We develop a low-input (100 ng), low-cost, and amplification-free library-generation method for PacBio sequencing (LILAP) using Tn5-based tagmentation and DNA circularization within one tube. We test LILAP with two Drosophila melanogaster individuals, and generate near-complete genomes, surpassing preexisting single-fly genomes. By analyzing variations in these two genomes, we characterize mutational processes: complex transpositions (transposon insertions together with extra duplications and/or deletions) prefer regions characterized by non-B DNA structures, and gene conversion of transposons occurs on both DNA and RNA levels. Concurrently, we generate two complete assemblies for the endosymbiotic bacterium Wolbachia in these flies and similarly detect transposon conversion. Thus, LILAP promises a broad PacBio sequencing adoption for not only mutational studies of flies and their symbionts but also explorations of other small organisms or precious samples.

Suggested Citation

  • Hangxing Jia & Shengjun Tan & Yingao Cai & Yanyan Guo & Jieyu Shen & Yaqiong Zhang & Huijing Ma & Qingzhu Zhang & Jinfeng Chen & Gexia Qiao & Jue Ruan & Yong E. Zhang, 2024. "Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49992-6
    DOI: 10.1038/s41467-024-49992-6
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    References listed on IDEAS

    as
    1. Matthew A. Lawlor & Weihuan Cao & Christopher E. Ellison, 2021. "A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Mahul Chakraborty & J. J. Emerson & Stuart J. Macdonald & Anthony D. Long, 2019. "Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    3. Qingbo Wang & Emma Pierce-Hoffman & Beryl B. Cummings & Jessica Alföldi & Laurent C. Francioli & Laura D. Gauthier & Andrew J. Hill & Anne H. O’Donnell-Luria & Konrad J. Karczewski & Daniel G. MacArth, 2020. "Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    4. Mitchell R. Vollger & Philip C. Dishuck & William T. Harvey & William S. DeWitt & Xavi Guitart & Michael E. Goldberg & Allison N. Rozanski & Julian Lucas & Mobin Asri & Katherine M. Munson & Alexandra, 2023. "Increased mutation and gene conversion within human segmental duplications," Nature, Nature, vol. 617(7960), pages 325-334, May.
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