Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing
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 o...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co. Ltd.
2022-11-01
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| Series: | Fundamental Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667325822001145 |
| _version_ | 1797976324587913216 |
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| author | Xiaofei Yang Xixi Zhao Shoufang Qu Peng Jia Bo Wang Shenghan Gao Tun Xu Wenxin Zhang Jie Huang Kai Ye |
| author_facet | Xiaofei Yang Xixi Zhao Shoufang Qu Peng Jia Bo Wang Shenghan Gao Tun Xu Wenxin Zhang Jie Huang Kai Ye |
| author_sort | Xiaofei Yang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T04:49:08Z |
| format | Article |
| id | doaj.art-b8ae0c4e73e84c55b8804e590dd9d82a |
| institution | Directory Open Access Journal |
| issn | 2667-3258 |
| language | English |
| last_indexed | 2024-04-11T04:49:08Z |
| publishDate | 2022-11-01 |
| publisher | KeAi Communications Co. Ltd. |
| record_format | Article |
| series | Fundamental Research |
| spelling | doaj.art-b8ae0c4e73e84c55b8804e590dd9d82a2022-12-27T04:43:18ZengKeAi Communications Co. Ltd.Fundamental Research2667-32582022-11-0126946953Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencingXiaofei Yang0Xixi Zhao1Shoufang Qu2Peng Jia3Bo Wang4Shenghan Gao5Tun Xu6Wenxin Zhang7Jie Huang8Kai Ye9Genome 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, ChinaGenome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, ChinaNational Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili, Dongcheng District, Beijing 102629, ChinaMOE 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, ChinaMOE 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, ChinaMOE 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, ChinaMOE 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, ChinaNational Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili, Dongcheng District, Beijing 102629, ChinaNational Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili, Dongcheng District, Beijing 102629, China; Corresponding authors.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.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.http://www.sciencedirect.com/science/article/pii/S2667325822001145Genome assemblyHiFi readsHuman genomeHaplotype-resolvedChinese HanMutation landscape |
| spellingShingle | Xiaofei Yang Xixi Zhao Shoufang Qu Peng Jia Bo Wang Shenghan Gao Tun Xu Wenxin Zhang Jie Huang Kai Ye Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing Fundamental Research Genome assembly HiFi reads Human genome Haplotype-resolved Chinese Han Mutation landscape |
| title | Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing |
| title_full | Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing |
| title_fullStr | Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing |
| title_full_unstemmed | Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing |
| title_short | Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing |
| title_sort | haplotype resolved chinese male genome assembly based on high fidelity sequencing |
| topic | Genome assembly HiFi reads Human genome Haplotype-resolved Chinese Han Mutation landscape |
| url | http://www.sciencedirect.com/science/article/pii/S2667325822001145 |
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