{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T12:32:35Z","timestamp":1793190755430,"version":"4.5.0"},"reference-count":88,"publisher":"National Academy of Sciences","issue":"8","license":[{"start":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T00:00:00Z","timestamp":1676246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["J4477-B"],"award-info":[{"award-number":["J4477-B"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2023,2,21]]},"abstract":"<jats:p>\n                    Microchromosomes are prevalent in nonmammalian vertebrates [P. D. Waters\n                    <jats:italic>et al.<\/jats:italic>\n                    ,\n                    <jats:italic>Proc. Natl. Acad. Sci. U.S.A.<\/jats:italic>\n                    <jats:bold>118<\/jats:bold>\n                    (2021)], but a few of them are missing in bird genome assemblies. Here, we present a new chicken reference genome containing all autosomes, a Z and a W chromosome, with all gaps closed except for the W. We identified ten small microchromosomes (termed dot chromosomes) with distinct sequence and epigenetic features, among which six were newly assembled. Those dot chromosomes exhibit extremely high GC content and a high level of DNA methylation and are enriched for housekeeping genes. The pericentromeric heterochromatin of dot chromosomes is disproportionately large and continues to expand with the proliferation of satellite DNA and testis-expressed genes. Our analyses revealed that the 41-bp CNM repeat frequently forms higher-order repeats (HORs) at the centromeres of acrocentric chromosomes. The centromere core regions where the kinetochore attaches often encompass telomeric sequence (TTAGGG)n, and in a one of the dot chromosomes, the centromere core recruits an endogenous retrovirus (ERV). We further demonstrate that the W chromosome shares some common features with dot chromosomes, having large arrays of hypermethylated tandem repeats. Finally, using the complete chicken chromosome models, we reconstructed a fine picture of chordate karyotype evolution, revealing frequent chromosomal fusions before and after vertebrate whole-genome duplications. Our sequence and epigenetic characterization of chicken chromosomes shed insights into the understanding of vertebrate genome evolution and chromosome biology.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2216641120","type":"journal-article","created":{"date-parts":[[2023,2,13]],"date-time":"2023-02-13T15:11:51Z","timestamp":1676301111000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":168,"title":["Evolutionary analysis of a complete chicken genome"],"prefix":"10.1073","volume":"120","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8908-0355","authenticated-orcid":false,"given":"Zhen","family":"Huang","sequence":"first","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China"},{"name":"Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China"},{"name":"Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou 350108, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4192-7083","authenticated-orcid":false,"given":"Zaoxu","family":"Xu","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China"},{"name":"Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, College of Life Sciences and Technology, Longdong University, Qingyang, Gansu Province 745000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5738-4186","authenticated-orcid":false,"given":"Hao","family":"Bai","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China"},{"name":"Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2513-5983","authenticated-orcid":false,"given":"Yongji","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Oceanography, Minjiang University, Fuzhou 350108, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Na","family":"Kang","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoting","family":"Ding","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0420-1769","authenticated-orcid":false,"given":"Jing","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8590-2991","authenticated-orcid":false,"given":"Haoran","family":"Luo","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China"},{"name":"Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3447-2316","authenticated-orcid":false,"given":"Chentao","family":"Yang","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanjun","family":"Chen","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qixin","family":"Guo","sequence":"additional","affiliation":[{"name":"Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China"},{"name":"Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingzhan","family":"Xue","sequence":"additional","affiliation":[{"name":"Aquaculture and Genetic breeding laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueping","family":"Zhang","sequence":"additional","affiliation":[{"name":"Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Xu","sequence":"additional","affiliation":[{"name":"Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meiling","family":"Chen","sequence":"additional","affiliation":[{"name":"Fujian Key Laboratory of Developmental and Neural Biology, College 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Huang Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. bioRxiv [Preprint] (2022). https:\/\/doi.org\/10.1101\/2022.01.04.475009 (Accessed on 5\u00a0January 2022).","DOI":"10.1101\/2022.01.04.475009"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24573-z"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.8.6.621"},{"key":"e_1_3_4_18_2","doi-asserted-by":"crossref","unstructured":"M. Li De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on micro-chromosomes and sub-telomeric regions. Mol. Biol. 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Luo Retrieving the near-complete genome of a threatened bird from wild frozen samples. bioRxiv [Preprint] (2022). https:\/\/doi.org\/10.1101\/2022.12.22.521577 (Accessed 22 December 2022).","DOI":"10.1101\/2022.12.22.521577"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature05621"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04267-9"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz891"},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-01056-5"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0831-x"},{"key":"e_1_3_4_57_2","first-page":"999","article-title":"Iterative correction of Hi-C data reveals hallmarks of chromosome organization","volume":"9","author":"Imakaev M.","year":"2012","unstructured":"M. Imakaev, G. Fudenberg, R. P. McCord, N. 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