1
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Jia P, Dong L, Yang X, Wang B, Bush SJ, Wang T, Lin J, Wang S, Zhao X, Xu T, Che Y, Dang N, Ren L, Zhang Y, Wang X, Liang F, Wang Y, Ruan J, Xia H, Zheng Y, Shi L, Lv Y, Wang J, Ye K. Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet. Genome Biol 2023; 24:277. [PMID: 38049885 PMCID: PMC10694985 DOI: 10.1186/s13059-023-03116-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet, comprising two monozygotic twin daughters and their biological parents, using four short and long sequencing platforms (Illumina, BGI, PacBio, and Oxford Nanopore Technology). RESULTS The long reads from the monozygotic twin daughters are phased into paternal and maternal haplotypes using the parent-child genetic map and for each haplotype. We also use long reads to generate haplotype-resolved whole-genome assemblies with completeness and continuity exceeding that of GRCh38. Using this Quartet, we comprehensively catalogue the human variant landscape, generating a dataset of 3,962,453 SNVs, 886,648 indels (< 50 bp), 9726 large deletions (≥ 50 bp), 15,600 large insertions (≥ 50 bp), 40 inversions, 31 complex structural variants, and 68 de novo mutations which are shared between the monozygotic twin daughters. Variants underrepresented in previous benchmarks owing to their complexity-including those located at long repeat regions, complex structural variants, and de novo mutations-are systematically examined in this study. CONCLUSIONS In summary, this study provides high-quality haplotype-resolved assemblies and a comprehensive set of benchmarking resources for two Chinese monozygotic twin samples which, relative to existing benchmarks, offers expanded genomic coverage and insight into complex variant categories.
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Affiliation(s)
- Peng Jia
- National Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lianhua Dong
- National Institute of Metrology, Beijing, 100029, China
| | - Xiaofei Yang
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Stephen J Bush
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Tingjie Wang
- National Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jiadong Lin
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Songbo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xixi Zhao
- National Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Tun Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yizhuo Che
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ningxin Dang
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China
| | - Yujing Zhang
- National Institute of Metrology, Beijing, 100029, China
| | - Xia Wang
- National Institute of Metrology, Beijing, 100029, China
| | - Fan Liang
- GrandOmics Biosciences, Beijing, 100089, China
| | - Yang Wang
- GrandOmics Biosciences, Beijing, 100089, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Han Xia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China
| | - Yi Lv
- National Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Jing Wang
- National Institute of Metrology, Beijing, 100029, China.
| | - Kai Ye
- National Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
- Faculty of Science, Leiden University, Leiden, 2311EZ, The Netherlands.
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2
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Zhang X. T2T-YAO Reference Genome of Han Chinese - New Step in Advancing Precision Medicine in China. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1083-1084. [PMID: 37742995 PMCID: PMC11082255 DOI: 10.1016/j.gpb.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing 100005, China.
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3
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He Y, Chu Y, Guo S, Hu J, Li R, Zheng Y, Ma X, Du Z, Zhao L, Yu W, Xue J, Bian W, Yang F, Chen X, Zhang P, Wu R, Ma Y, Shao C, Chen J, Wang J, Li J, Wu J, Hu X, Long Q, Jiang M, Ye H, Song S, Li G, Wei Y, Xu Y, Ma Y, Chen Y, Wang K, Bao J, Xi W, Wang F, Ni W, Zhang M, Yu Y, Li S, Kang Y, Gao Z. T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1085-1100. [PMID: 37595788 PMCID: PMC11082261 DOI: 10.1016/j.gpb.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Since its initial release in 2001, the human reference genome has undergone continuous improvement in quality, and the recently released telomere-to-telomere (T2T) version - T2T-CHM13 - reaches its highest level of continuity and accuracy after 20 years of effort by working on a simplified, nearly homozygous genome of a hydatidiform mole cell line. Here, to provide an authentic complete diploid human genome reference for the Han Chinese, the largest population in the world, we assembled the genome of a male Han Chinese individual, T2T-YAO, which includes T2T assemblies of all the 22 + X + M and 22 + Y chromosomes in both haploids. The quality of T2T-YAO is much better than those of all currently available diploid assemblies, and its haploid version, T2T-YAO-hp, generated by selecting the better assembly for each autosome, reaches the top quality of fewer than one error per 29.5 Mb, even higher than that of T2T-CHM13. Derived from an individual living in the aboriginal region of the Han population, T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors. Each haplotype of T2T-YAO possesses ∼ 330-Mb exclusive sequences, ∼ 3100 unique genes, and tens of thousands of nucleotide and structural variations as compared with CHM13, highlighting the necessity of a population-stratified reference genome. The construction of T2T-YAO, an accurate and authentic representative of the Chinese population, would enable precise delineation of genomic variations and advance our understandings in the hereditability of diseases and phenotypes, especially within the context of the unique variations of the Chinese population.
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Affiliation(s)
- Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Shuming Guo
- Linfen Clinical Medicine Research Center, Linfen 041000, China; Institute of Chest and Lung Diseases, Shanxi Medical University, Taiyuan 030001, China
| | - Jiang Hu
- GrandOmics Biosciences Co., Ltd, Wuhan 430076, China
| | - Ran Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Yali Zheng
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Zhenglin Du
- Institute of PSI Genomics, Wenzhou 325024, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Jianbo Xue
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Wenjie Bian
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Feifei Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Xi Chen
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Pingan Zhang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Rihan Wu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Yifan Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Changjun Shao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jing Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jiwei Li
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Jing Wu
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Xiaoyi Hu
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Qiuyue Long
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Mingzheng Jiang
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Hongli Ye
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Shixu Song
- Department of Respiratory, Critical Care and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361101, China
| | - Guangyao Li
- Linfen Clinical Medicine Research Center, Linfen 041000, China
| | - Yue Wei
- Linfen Clinical Medicine Research Center, Linfen 041000, China
| | - Yu Xu
- Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, China
| | - Yanliang Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Yanwen Chen
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Keqiang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Jing Bao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Wen Xi
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Fang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Wentao Ni
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Moqin Zhang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Yan Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Shengnan Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100490, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China; Institute of Chest and Lung Diseases, Shanxi Medical University, Taiyuan 030001, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing 100101, China.
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4
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Gao Y, Yang X, Chen H, Tan X, Yang Z, Deng L, Wang B, Kong S, Li S, Cui Y, Lei C, Wang Y, Pan Y, Ma S, Sun H, Zhao X, Shi Y, Yang Z, Wu D, Wu S, Zhao X, Shi B, Jin L, Hu Z, Lu Y, Chu J, Ye K, Xu S. A pangenome reference of 36 Chinese populations. Nature 2023:10.1038/s41586-023-06173-7. [PMID: 37316654 PMCID: PMC10322713 DOI: 10.1038/s41586-023-06173-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/05/2023] [Indexed: 06/16/2023]
Abstract
Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form, but populations of Asian ancestry are underrepresented. Here we present data from the first phase of the Chinese Pangenome Consortium, including a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With an average 30.65× high-fidelity long-read sequence coverage, an average contiguity N50 of more than 35.63 megabases and an average total size of 3.01 gigabases, the CPC core assemblies add 189 million base pairs of euchromatic polymorphic sequences and 1,367 protein-coding gene duplications to GRCh38. We identified 15.9 million small variants and 78,072 structural variants, of which 5.9 million small variants and 34,223 structural variants were not reported in a recently released pangenome reference1. The Chinese Pangenome Consortium data demonstrate a remarkable increase in the discovery of novel and missing sequences when individuals are included from underrepresented minority ethnic groups. The missing reference sequences were enriched with archaic-derived alleles and genes that confer essential functions related to keratinization, response to ultraviolet radiation, DNA repair, immunological responses and lifespan, implying great potential for shedding new light on human evolution and recovering missing heritability in complex disease mapping.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinjiang Tan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoqing Yang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, China
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Baonan Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Shuang Kong
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Songyang Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Yuhang Cui
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Chang Lei
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yimin Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sen Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hao Sun
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, China
| | - Xiaohan Zhao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Yingbing Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyi Yang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, International Joint Center of Genomics of Jiangsu Province School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xingming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Ministry of Education Key (MOE) Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science Fudan University, Shanghai, China
| | - Binyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Jiayou Chu
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, China.
| | - Kai Ye
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, International Joint Center of Genomics of Jiangsu Province School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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5
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Chao KH, Zimin AV, Pertea M, Salzberg SL. The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual. G3 (BETHESDA, MD.) 2023; 13:jkac321. [PMID: 36630290 PMCID: PMC9997556 DOI: 10.1093/g3journal/jkac321] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 01/12/2023]
Abstract
We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. We organized the sequence into chromosomes and filled in gaps using the recently completed T2T-CHM13 genome as a guide, yielding a gap-free genome, Han1, containing 3,099,707,698 bases. Using the T2T-CHM13 annotation as a reference, we mapped all genes onto the Han1 genome and identified additional gene copies, generating a total of 60,708 putative genes, of which 20,003 are protein-coding. A comprehensive comparison between the genes revealed that 235 protein-coding genes were substantially different between the individuals, with frameshifts or truncations affecting the protein-coding sequence. Most of these were heterozygous variants in which one gene copy was unaffected. This represents the first gene-level comparison between two finished, annotated individual human genomes.
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Affiliation(s)
- Kuan-Hao Chao
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA
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6
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Wang X, Song Y, Xie H, Zi F, Chen S, Luo S. Complete Mitogenome of the Triplophysa bombifrons: Comparative Analysis and Phylogenetic Relationships among the Members of Triplophysa. Genes (Basel) 2023; 14:genes14010128. [PMID: 36672869 PMCID: PMC9858811 DOI: 10.3390/genes14010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of Triplophysa bombifrons via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the Triplophysa genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of T. bombifrons was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for cox1, and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the Triplophysa genus can be divided into 4 main clades and demonstrated that T. bombifrons and T. tenuis are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes.
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Affiliation(s)
- Xinyue Wang
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, China
| | - Yong Song
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, China
| | - Haoyang Xie
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, China
| | - Fangze Zi
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, China
| | - Shengao Chen
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, China
- Correspondence: (S.C.); (S.L.)
| | - Site Luo
- School of Life Sciences, Xiamen University, Xiamen 361102, China
- Correspondence: (S.C.); (S.L.)
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Hai DM, Yen DT, Liem PT, Tam BM, Huong DTT, Hang BTB, Hieu DQ, Garigliany MM, Coppieters W, Kestemont P, Phuong NT, Farnir F. A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data. Genes (Basel) 2022; 13:genes13050923. [PMID: 35627308 PMCID: PMC9141817 DOI: 10.3390/genes13050923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022] Open
Abstract
The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (Pangasianodon hypophthalmus), a commercially important species cultured mainly in Vietnam, integrating HiFi reads and Hi-C data. A 788.4 Mb genome containing 381 scaffolds with an N50 length of 21.8 Mb has been obtained from HiFi reads. These scaffolds have been further ordered and clustered into 30 chromosome groups, ranging from 1.4 to 57.6 Mb, based on Hi-C data. The present updated assembly has a contig N50 of 14.7 Mb, representing a 245-fold and 4.2-fold improvement over the previous Illumina and Illumina-Nanopore-Hi-C based version, respectively. In addition, the proportion of repeat elements and BUSCO genes identified in our genome is remarkably higher than in the two previously released striped catfish genomes. These results highlight the power of using HiFi reads to assemble the highly repetitive regions and to improve the quality of genome assembly. The updated, high-quality genome assembled in this work will provide a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of striped catfish.
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Affiliation(s)
- Dao Minh Hai
- FARAH/Sustainable Animal Production, Faculty of Veterinary Medicine, University of Liege (B43), 4000 Liege, Belgium;
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Duong Thuy Yen
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Pham Thanh Liem
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Bui Minh Tam
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Do Thi Thanh Huong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Bui Thi Bich Hang
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Dang Quang Hieu
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Mutien-Marie Garigliany
- FARAH/Veterinary Public Health, Faculty of Veterinary Medicine, University of Liege (B43), 4000 Liege, Belgium;
| | | | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology, Institute of Life, Earth & Environnment, University of Namur, rue de Bruxelles 61, 5000 Namur, Belgium;
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Frédéric Farnir
- FARAH/Sustainable Animal Production, Faculty of Veterinary Medicine, University of Liege (B43), 4000 Liege, Belgium;
- Correspondence:
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