{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T01:51:37Z","timestamp":1793238697703,"version":"4.5.0"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T00:00:00Z","timestamp":1716768000000},"content-version":"vor","delay-in-days":285,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2023,8,16]],"date-time":"2023-08-16T00:00:00Z","timestamp":1692144000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,8,14]],"date-time":"2023-08-14T00:00:00Z","timestamp":1691971200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"Linfen Soft Science Research Project","award":["2126"],"award-info":[{"award-number":["2126"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970568"],"award-info":[{"award-number":["31970568"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFC2301000"],"award-info":[{"award-number":["2021YFC2301000"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National and Provincial Key Clinical Specialty Capacity Building Project 2020","award":["RDGS2022-11"],"award-info":[{"award-number":["RDGS2022-11"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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 \u2014 T2T-CHM13 \u2014 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 \u223c 330-Mb exclusive sequences, \u223c 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.<\/jats:p>","DOI":"10.1016\/j.gpb.2023.08.001","type":"journal-article","created":{"date-parts":[[2023,8,16]],"date-time":"2023-08-16T11:55:21Z","timestamp":1692186921000},"page":"1085-1100","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":68,"title":["T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese"],"prefix":"10.1093","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4164-2478","authenticated-orcid":false,"given":"Yukun","family":"He","sequence":"first","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9349-4307","authenticated-orcid":false,"given":"Yanan","family":"Chu","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7931-3725","authenticated-orcid":false,"given":"Shuming","family":"Guo","sequence":"additional","affiliation":[{"name":"Linfen Clinical Medicine Research Center , Linfen, 041000 , China"},{"name":"Institute of Chest and Lung Diseases, Shanxi Medical University , Taiyuan, 030001 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8521-9161","authenticated-orcid":false,"given":"Jiang","family":"Hu","sequence":"additional","affiliation":[{"name":"GrandOmics Biosciences Co., Ltd , , Wuhan, 430076 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5085-0463","authenticated-orcid":false,"given":"Ran","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0359-2799","authenticated-orcid":false,"given":"Yali","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6356-6584","authenticated-orcid":false,"given":"Xinqian","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2147-3475","authenticated-orcid":false,"given":"Zhenglin","family":"Du","sequence":"additional","affiliation":[{"name":"Institute of PSI Genomics , Wenzhou, 325024 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-9016-0106","authenticated-orcid":false,"given":"Lili","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3455-3087","authenticated-orcid":false,"given":"Wenyi","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2531-7808","authenticated-orcid":false,"given":"Jianbo","family":"Xue","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6716-4489","authenticated-orcid":false,"given":"Wenjie","family":"Bian","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1830-5978","authenticated-orcid":false,"given":"Feifei","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5421-8704","authenticated-orcid":false,"given":"Xi","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0524-4322","authenticated-orcid":false,"given":"Pingan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4902-9767","authenticated-orcid":false,"given":"Rihan","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-7009-4341","authenticated-orcid":false,"given":"Yifan","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5836-9447","authenticated-orcid":false,"given":"Changjun","family":"Shao","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2252-8001","authenticated-orcid":false,"given":"Jing","family":"Chen","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0434-0139","authenticated-orcid":false,"given":"Jian","family":"Wang","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4652-8842","authenticated-orcid":false,"given":"Jiwei","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7075-3687","authenticated-orcid":false,"given":"Jing","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3904-0547","authenticated-orcid":false,"given":"Xiaoyi","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5361-3260","authenticated-orcid":false,"given":"Qiuyue","family":"Long","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-3273-0012","authenticated-orcid":false,"given":"Mingzheng","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-7538-2668","authenticated-orcid":false,"given":"Hongli","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-0689-6869","authenticated-orcid":false,"given":"Shixu","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Respiratory, Critical Care and Sleep Medicine, Xiang\u2019an Hospital of Xiamen University, School of Medicine, Xiamen University , Xiamen, 361101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1468-2163","authenticated-orcid":false,"given":"Guangyao","family":"Li","sequence":"additional","affiliation":[{"name":"Linfen Clinical Medicine Research Center , Linfen, 041000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4213-6796","authenticated-orcid":false,"given":"Yue","family":"Wei","sequence":"additional","affiliation":[{"name":"Linfen Clinical Medicine Research Center , Linfen, 041000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1297-1312","authenticated-orcid":false,"given":"Yu","family":"Xu","sequence":"additional","affiliation":[{"name":"Beijing Jishuitan Hospital, Capital Medical University , Beijing, 100035 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8491-391X","authenticated-orcid":false,"given":"Yanliang","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1173-2096","authenticated-orcid":false,"given":"Yanwen","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-5157-2565","authenticated-orcid":false,"given":"Keqiang","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2273-4577","authenticated-orcid":false,"given":"Jing","family":"Bao","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1058-3345","authenticated-orcid":false,"given":"Wen","family":"Xi","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8219-4637","authenticated-orcid":false,"given":"Fang","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0687-5196","authenticated-orcid":false,"given":"Wentao","family":"Ni","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5811-9966","authenticated-orcid":false,"given":"Moqin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0898-7951","authenticated-orcid":false,"given":"Yan","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-4034-9930","authenticated-orcid":false,"given":"Shengnan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5196-0376","authenticated-orcid":false,"given":"Yu","family":"Kang","sequence":"additional","affiliation":[{"name":"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"},{"name":"University of Chinese Academy of Sciences , Beijing, 100490 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7415-1416","authenticated-orcid":false,"given":"Zhancheng","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Respiratory and Critical Care Medicine, Peking University People\u2019s Hospital , Beijing, 100044 , China"},{"name":"Institute of Chest and Lung Diseases, Shanxi Medical University , Taiyuan, 030001 , China"},{"name":"Beijing Key Laboratory of Genome and Precision Medicine Technologies , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,8,16]]},"reference":[{"key":"2024052704423077400_b0005","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2024052704423077400_b0010","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","article-title":"The sequence of the human genome","volume":"291","author":"Venter","year":"2001","journal-title":"Science"},{"key":"2024052704423077400_b0015","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nature03001","article-title":"Finishing the euchromatic sequence of the human genome","volume":"431","author":"International Human Genome Sequencing Consortium.","year":"2004","journal-title":"Nature"},{"key":"2024052704423077400_b0020","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science"},{"key":"2024052704423077400_b0025","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1038\/s41592-022-01440-3","article-title":"Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies","volume":"19","author":"Mc Cartney","year":"2022","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0030","doi-asserted-by":"crossref","first-page":"eabj5089","DOI":"10.1126\/science.abj5089","article-title":"Epigenetic patterns in a complete human genome","volume":"376","author":"Gershman","year":"2022","journal-title":"Science"},{"key":"2024052704423077400_b0035","doi-asserted-by":"crossref","first-page":"eabj6965","DOI":"10.1126\/science.abj6965","article-title":"Segmental duplications and their variation in a complete human genome","volume":"376","author":"Vollger","year":"2022","journal-title":"Science"},{"key":"2024052704423077400_b0040","doi-asserted-by":"crossref","first-page":"eabl3533","DOI":"10.1126\/science.abl3533","article-title":"A complete reference genome improves analysis of human genetic variation","volume":"376","author":"Aganezov","year":"2022","journal-title":"Science"},{"key":"2024052704423077400_b0045","doi-asserted-by":"crossref","first-page":"eabl4178","DOI":"10.1126\/science.abl4178","article-title":"Complete genomic and epigenetic maps of human centromeres","volume":"376","author":"Altemose","year":"2022","journal-title":"Science"},{"key":"2024052704423077400_b0050","doi-asserted-by":"crossref","first-page":"eabk3112","DOI":"10.1126\/science.abk3112","article-title":"From telomere to telomere: the transcriptional and epigenetic state of human repeat elements","volume":"376","author":"Hoyt","year":"2022","journal-title":"Science"},{"key":"2024052704423077400_b0055","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1126\/science.abo5367","article-title":"A next-generation human genome sequence","volume":"376","author":"Church","year":"2022","journal-title":"Science"},{"key":"2024052704423077400_b0060","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1006\/geno.2001.6676","article-title":"Paternal origins of complete hydatidiform moles proven by whole genome single-nucleotide polymorphism haplotyping","volume":"79","author":"Fan","year":"2002","journal-title":"Genomics"},{"key":"2024052704423077400_b0065","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","article-title":"A draft human pangenome reference","volume":"617","author":"Liao","year":"2023","journal-title":"Nature"},{"key":"2024052704423077400_b0070","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41586-023-06173-7","article-title":"A pangenome reference of 36 Chinese populations","volume":"619","author":"Gao","year":"2023","journal-title":"Nature"},{"key":"2024052704423077400_b0075","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41586-022-05325-5","article-title":"Semi-automated assembly of high-quality diploid human reference genomes","volume":"611","author":"Jarvis","year":"2022","journal-title":"Nature"},{"key":"2024052704423077400_b0080","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.gpb.2019.07.002","article-title":"Whole genome analyses of Chinese population and de novo assembly of a Northern Han genome","volume":"17","author":"Du","year":"2019","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024052704423077400_b0085","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1016\/j.fmre.2022.02.005","article-title":"Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing","volume":"2","author":"Yang","year":"2022","journal-title":"Fundam Res"},{"key":"2024052704423077400_b0090","doi-asserted-by":"crossref","first-page":"jkac321","DOI":"10.1093\/g3journal\/jkac321","article-title":"The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual","volume":"13","author":"Chao","year":"2023","journal-title":"G3 (Bethesda)"},{"key":"2024052704423077400_b0095","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/s41422-023-00849-5","article-title":"The complete and fully-phased diploid genome of a male Han Chinese","volume":"33","author":"Yang","year":"2023","journal-title":"Cell Res"},{"key":"2024052704423077400_b0100","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1101\/gr.180893.114","article-title":"Single haplotype assembly of the human genome from a hydatidiform mole","volume":"24","author":"Steinberg","year":"2014","journal-title":"Genome Res"},{"key":"2024052704423077400_b0105","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","article-title":"Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome","volume":"37","author":"Wenger","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2024052704423077400_b0110","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1101\/gr.263566.120","article-title":"HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads","volume":"30","author":"Nurk","year":"2020","journal-title":"Genome Res"},{"key":"2024052704423077400_b0115","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024052704423077400_b0120","doi-asserted-by":"crossref","first-page":"e1007273","DOI":"10.1371\/journal.pcbi.1007273","article-title":"Integrating Hi-C links with assembly graphs for chromosome-scale assembly","volume":"15","author":"Ghurye","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"2024052704423077400_b0125","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/nbt.2303","article-title":"Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly","volume":"30","author":"Lam","year":"2012","journal-title":"Nat Biotechnol"},{"key":"2024052704423077400_b0130","first-page":"mgen000936","article-title":"Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae","volume":"9","author":"Foster-Nyarko","year":"2023","journal-title":"Microb Genom"},{"key":"2024052704423077400_b0135","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1038\/s41587-022-01220-6","article-title":"Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads","volume":"40","author":"Bankevich","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2024052704423077400_b0140","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1038\/s41587-023-01662-6","article-title":"Telomere-to-telomere assembly of diploid chromosomes with Verkko","volume":"41","author":"Rautiainen","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2024052704423077400_b0145","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/s41592-022-01457-8","article-title":"Long-read mapping to repetitive reference sequences using Winnowmap2","volume":"19","author":"Jain","year":"2022","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0150","doi-asserted-by":"crossref","DOI":"10.1093\/gpbjnl\/qzad009","article-title":"NextPolish2: a repeat-aware polishing tool for genomes assembled using HiFi long reads","volume":"22","author":"Hu","year":"2024","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024052704423077400_b0155","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A universal SNP and small-indel variant caller using deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024052704423077400_b0160","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1038\/s41592-021-01299-w","article-title":"Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads","volume":"18","author":"Shafin","year":"2021","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0165","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/s41592-018-0001-7","article-title":"Accurate detection of complex structural variations using single-molecule sequencing","volume":"15","author":"Sedlazeck","year":"2018","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0170","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1038\/s41592-022-01445-y","article-title":"Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation","volume":"19","author":"Formenti","year":"2022","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0175","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/s41592-022-01753-3","article-title":"Jasmine and Iris: population-scale structural variant comparison and analysis","volume":"20","author":"Kirsche","year":"2023","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0180","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024052704423077400_b0185","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2024052704423077400_b0190","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies","volume":"21","author":"Rhie","year":"2020","journal-title":"Genome Biol"},{"key":"2024052704423077400_b0195","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.ajhg.2013.06.020","article-title":"RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference","volume":"93","author":"Maples","year":"2013","journal-title":"Am J Hum Genet"},{"key":"2024052704423077400_b0200","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"1000 Genomes Project Consortium","year":"2015","journal-title":"Nature"},{"key":"2024052704423077400_b0205","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1093\/molbev\/msx177","article-title":"Genetic history of Xinjiang\u2019s Uyghurs suggests Bronze Age multiple-way contacts in Eurasia","volume":"34","author":"Feng","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2024052704423077400_b0210","first-page":"088716","article-title":"Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men","author":"Poznik","year":"2016","journal-title":"bioRxiv"},{"key":"2024052704423077400_b0215","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1038\/nature01722","article-title":"The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes","volume":"423","author":"Skaletsky","year":"2003","journal-title":"Nature"},{"key":"2024052704423077400_b0220","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s40169-015-0060-7","article-title":"Human chromosome Y and haplogroups; introducing YDHS database","volume":"4","author":"Tiirikka","year":"2015","journal-title":"Clin Transl Med"},{"key":"2024052704423077400_b0225","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1086\/444436","article-title":"Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3\u2013M122","volume":"77","author":"Shi","year":"2005","journal-title":"Am J Hum Genet"},{"key":"2024052704423077400_b0230","doi-asserted-by":"crossref","first-page":"e105691","DOI":"10.1371\/journal.pone.0105691","article-title":"Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers","volume":"9","author":"Yan","year":"2014","journal-title":"PLoS One"},{"key":"2024052704423077400_b0235","doi-asserted-by":"crossref","first-page":"2700","DOI":"10.1038\/s41467-020-16557-2","article-title":"Ancient genomes from northern China suggest links between subsistence changes and human migration","volume":"11","author":"Ning","year":"2020","journal-title":"Nat Commun"},{"key":"2024052704423077400_b0240","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"2024052704423077400_b0245","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1038\/s41586-023-05895-y","article-title":"Increased mutation and gene conversion within human segmental duplications","volume":"617","author":"Vollger","year":"2023","journal-title":"Nature"},{"key":"2024052704423077400_b0250","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.tig.2023.02.008","article-title":"Repetitive elements in aging and neurodegeneration","volume":"39","author":"Copley","year":"2023","journal-title":"Trends Genet"},{"key":"2024052704423077400_b0255","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1101\/gr.233460.117","article-title":"Comparative annotation toolkit (CAT) \u2014 simultaneous clade and personal genome annotation","volume":"28","author":"Fiddes","year":"2018","journal-title":"Genome Res"},{"key":"2024052704423077400_b0260","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1093\/bioinformatics\/btaa1016","article-title":"Liftoff: accurate mapping of gene annotations","volume":"37","author":"Shumate","year":"2021","journal-title":"Bioinformatics"},{"key":"2024052704423077400_b0265","doi-asserted-by":"crossref","first-page":"D942","DOI":"10.1093\/nar\/gkac1071","article-title":"GENCODE: reference annotation for the human and mouse genomes in 2023","volume":"51","author":"Frankish","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024052704423077400_b0270","doi-asserted-by":"crossref","first-page":"5519","DOI":"10.1093\/bioinformatics\/btaa1034","article-title":"SVIM-asm: structural variant detection from haploid and diploid genome assemblies","volume":"36","author":"Heller","year":"2020","journal-title":"Bioinformatics"},{"key":"2024052704423077400_b0275","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1186\/s13059-019-1911-0","article-title":"SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies","volume":"20","author":"Goel","year":"2019","journal-title":"Genome Biol"},{"key":"2024052704423077400_b0280","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1101\/gr.126037.111","article-title":"The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism","volume":"22","author":"Salm","year":"2012","journal-title":"Genome Res"},{"key":"2024052704423077400_b0285","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s41586-021-03420-7","article-title":"The structure, function and evolution of a complete human chromosome 8","volume":"593","author":"Logsdon","year":"2021","journal-title":"Nature"},{"key":"2024052704423077400_b0290","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1007\/s10577-014-9439-3","article-title":"Narrowing the localization of the region breakpoint in most frequent Robertsonian translocations","volume":"22","author":"Jarmuz-Szymczak","year":"2014","journal-title":"Chromosome Res"},{"key":"2024052704423077400_b0295","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/s41586-023-05976-y","article-title":"Recombination between heterologous human acrocentric chromosomes","volume":"617","author":"Guarracino","year":"2023","journal-title":"Nature"},{"key":"2024052704423077400_b0300","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/j.tig.2019.07.006","article-title":"Mechanisms of rDNA copy number maintenance","volume":"35","author":"Nelson","year":"2019","journal-title":"Trends Genet"},{"key":"2024052704423077400_b0305","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1101\/gr.275838.121","article-title":"The human ribosomal DNA array is composed of highly homogenized tandem clusters","volume":"31","author":"Hori","year":"2021","journal-title":"Genome Res"},{"key":"2024052704423077400_b0310","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/s41580-022-00573-9","article-title":"Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes","volume":"24","author":"Hori","year":"2023","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024052704423077400_b0315","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/s41586-023-06457-y","article-title":"The complete sequence of a human Y chromosome","volume":"621","author":"Rhie","year":"2023","journal-title":"Nature"},{"key":"2024052704423077400_b0320","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s41586-023-06425-6","article-title":"Assembly of 43 human Y chromosomes reveals extensive complexity and variation","volume":"621","author":"Hallast","year":"2023","journal-title":"Nature"},{"key":"2024052704423077400_b0325","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res"},{"key":"2024052704423077400_b0330","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/s41592-018-0236-3","article-title":"Long-read sequence and assembly of segmental duplications","volume":"16","author":"Vollger","year":"2019","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0335","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13015-022-00210-2","article-title":"Fast characterization of segmental duplication structure in multiple genome assemblies","volume":"17","author":"Iseric","year":"2022","journal-title":"Algorithms Mol Biol"},{"key":"2024052704423077400_b0340","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1101\/gr.199448.115","article-title":"A time- and cost-effective strategy to sequence mammalian Y chromosomes: an application to the de novo assembly of gorilla Y","volume":"26","author":"Tomaszkiewicz","year":"2016","journal-title":"Genome Res"},{"key":"2024052704423077400_b0345","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/s41586-020-2871-y","article-title":"Progressive Cactus is a multiple-genome aligner for the thousand-genome era","volume":"587","author":"Armstrong","year":"2020","journal-title":"Nature"},{"key":"2024052704423077400_b0350","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41592-018-0054-7","article-title":"A synthetic-diploid benchmark for accurate variant-calling evaluation","volume":"15","author":"Li","year":"2018","journal-title":"Nat Methods"},{"key":"2024052704423077400_b0355","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1003s00","article-title":"Using MUMmer to identify similar regions in large sequence sets","author":"Delcher","year":"2003","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024052704423077400_b0360","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2024052704423077400_b0365","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The Genome Sequence Archive Family: toward explosive data growth and diverse data types","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024052704423077400_b0370","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/j.gpb.2021.04.001","article-title":"Genome Warehouse: a public repository housing genome-scale data","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022923001006?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022923001006?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/21\/6\/1085\/57922358\/gpb_21_6_1085.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/21\/6\/1085\/57922358\/gpb_21_6_1085.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,26]],"date-time":"2024-10-26T03:09:02Z","timestamp":1729912142000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/21\/6\/1085\/7682052"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,16]]},"references-count":74,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,12,1]]}},"URL":"https:\/\/doi.org\/10.1016\/j.gpb.2023.08.001","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.07.17.549286","asserted-by":"object"}]},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,12]]},"published":{"date-parts":[[2023,8,16]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese","name":"articletitle","label":"Article Title"},{"value":"Genomics, Proteomics & Bioinformatics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.gpb.2023.08.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences \/ China National Center for Bioinformation and Genetics Society of China","name":"copyright","label":"Copyright"}]}}