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Long-read sequencing and de novo assembly of a Chinese genome

Author

Listed:
  • Lingling Shi

    (Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University
    Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University
    Co-innovation Center of Neuroregeneration, Nantong University)

  • Yunfei Guo

    (Zilkha Neurogenetic Institute, University of Southern California)

  • Chengliang Dong

    (Zilkha Neurogenetic Institute, University of Southern California)

  • John Huddleston

    (Howard Hughes Medical Institute, University of Washington)

  • Hui Yang

    (Zilkha Neurogenetic Institute, University of Southern California)

  • Xiaolu Han

    (Genetic, Molecular, and Cellular Biology Program, Keck School of Medicine, University of Southern California)

  • Aisi Fu

    (Wuhan Institute of Biotechnology)

  • Quan Li

    (Zilkha Neurogenetic Institute, University of Southern California)

  • Na Li

    (Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University)

  • Siyi Gong

    (Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University)

  • Katherine E. Lintner

    (The Ohio State University, and The Research Institute at Nationwide Children's Hospital)

  • Qiong Ding

    (Wuhan Institute of Biotechnology)

  • Zou Wang

    (Wuhan Institute of Biotechnology)

  • Jiang Hu

    (Nextomics Biosciences)

  • Depeng Wang

    (Nextomics Biosciences)

  • Feng Wang

    (School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology)

  • Lin Wang

    (Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Huazhong University of Science and Technology)

  • Gholson J. Lyon

    (Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory)

  • Yongtao Guan

    (USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine)

  • Yufeng Shen

    (Columbia University)

  • Oleg V. Evgrafov

    (Zilkha Neurogenetic Institute, University of Southern California
    Keck School of Medicine, University of Southern California)

  • James A. Knowles

    (Zilkha Neurogenetic Institute, University of Southern California
    Keck School of Medicine, University of Southern California)

  • Francoise Thibaud-Nissen

    (National Center for Biotechnology Information, U.S. National Library of Medicine)

  • Valerie Schneider

    (National Center for Biotechnology Information, U.S. National Library of Medicine)

  • Chack-Yung Yu

    (The Ohio State University, and The Research Institute at Nationwide Children's Hospital)

  • Libing Zhou

    (Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University
    Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University
    Co-innovation Center of Neuroregeneration, Nantong University)

  • Evan E. Eichler

    (Howard Hughes Medical Institute, University of Washington)

  • Kwok-Fai So

    (Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University
    Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University
    Co-innovation Center of Neuroregeneration, Nantong University
    The University of Hong Kong)

  • Kai Wang

    (Zilkha Neurogenetic Institute, University of Southern California
    Keck School of Medicine, University of Southern California)

Abstract

Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93 Gb (contig N50: 8.3 Mb, scaffold N50: 22.0 Mb, including 39.3 Mb N-bases), together with 206 Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8 Mb of HX1-specific sequences, including 4.1 Mb that are not present in previously reported Asian genomes. Furthermore, long-read sequencing of the transcriptome reveals novel spliced genes that are not annotated in GENCODE and are missed by short-read RNA-Seq. Our results imply that improved characterization of genome functional variation may require the use of a range of genomic technologies on diverse human populations.

Suggested Citation

  • Lingling Shi & Yunfei Guo & Chengliang Dong & John Huddleston & Hui Yang & Xiaolu Han & Aisi Fu & Quan Li & Na Li & Siyi Gong & Katherine E. Lintner & Qiong Ding & Zou Wang & Jiang Hu & Depeng Wang & , 2016. "Long-read sequencing and de novo assembly of a Chinese genome," Nature Communications, Nature, vol. 7(1), pages 1-10, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12065
    DOI: 10.1038/ncomms12065
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    Cited by:

    1. Zhikun Wu & Zehang Jiang & Tong Li & Chuanbo Xie & Liansheng Zhao & Jiaqi Yang & Shuai Ouyang & Yizhi Liu & Tao Li & Zhi Xie, 2021. "Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Xue Gao & Sheng Wang & Yan-Fen Wang & Shuang Li & Shi-Xin Wu & Rong-Ge Yan & Yi-Wen Zhang & Rui-Dong Wan & Zhen He & Ren-De Song & Xin-Quan Zhao & Dong-Dong Wu & Qi-En Yang, 2022. "Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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