Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

Xiaofei Yang; Xixi Zhao; Shoufang Qu; Peng Jia; Bo Wang; Shenghan Gao; Tun Xu; Wenxin Zhang; Jie Huang; Kai Ye

Fundamental Research (Nov 2022)

Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

Xiaofei Yang,
Xixi Zhao,
Shoufang Qu,
Peng Jia,
Bo Wang,
Shenghan Gao,
Tun Xu,
Wenxin Zhang,
Jie Huang,
Kai Ye

Affiliations

Xiaofei Yang: Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China; School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
Xixi Zhao: Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
Shoufang Qu: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili, Dongcheng District, Beijing 102629, China
Peng Jia: MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
Bo Wang: MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
Shenghan Gao: MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
Tun Xu: MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China
Wenxin Zhang: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili, Dongcheng District, Beijing 102629, China
Jie Huang: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili, Dongcheng District, Beijing 102629, China; Corresponding authors.
Kai Ye: Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, China; Faculty of Science, Leiden University, Leiden, The Netherlands; Corresponding authors.

Journal volume & issue: Vol. 2, no. 6
pp. 946 – 953

Abstract

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The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi and Hi-C. We assembled two high-quality haplotypes of the HJ genome (haplotype 1 (H1): 3.1 Gb, haplotype 2 (H2): 2.9 Gb). The continuity (H1: contig N50 = 28.2 Mb, H2: contig N50 = 25.9 Mb) and completeness (BUSCO: H1 = 94.9%, H2 = 93.5%) are substantially better than those of other Chinese genomes, for example, HX1, NH1.0, and YH2.0. By comparing HJ genome with GRCh38, we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2, respectively. In addition, we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2, respectively. Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.

Published in Fundamental Research

ISSN: 2667-3258 (Online)
Publisher: KeAi Communications Co. Ltd.
Country of publisher: China
LCC subjects: Science: Science (General)
Website: https://www.keaipublishing.com/en/journals/fundamental-research/

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