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

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, Feng Wang, Lin Wang, Gholson J. Lyon, Yongtao Guan, Yufeng Shen, Oleg V. Evgrafov, James A. Knowles, Francoise Thibaud-Nissen, Valerie Schneider, Chack-Yung Yu, Libing Zhou (), Evan E. Eichler, Kwok-Fai So () and Kai Wang ()
Additional contact information
Lingling Shi: Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan 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
James A. Knowles: Zilkha Neurogenetic Institute, 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
Evan E. Eichler: Howard Hughes Medical Institute, University of Washington
Kwok-Fai So: Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University
Kai Wang: Zilkha Neurogenetic Institute, University of Southern California

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms12065

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