{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T02:10:51Z","timestamp":1774923051537,"version":"3.50.1"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T00:00:00Z","timestamp":1665360000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key Research and Development Plan of China","award":["2021YFF1000100"],"award-info":[{"award-number":["2021YFF1000100"]}]},{"name":"Natural Science Foundation of Henan","award":["212300410093"],"award-info":[{"award-number":["212300410093"]}]},{"name":"Hubei Provincial Natural Science Foundation of China","award":["2019CFA014"],"award-info":[{"award-number":["2019CFA014"]}]},{"name":"Developing Bioinformatics Platform in Hainan Yazhou Bay Seed Lab","award":["JBGS-B21HJ0001"],"award-info":[{"award-number":["JBGS-B21HJ0001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Cotton is an important economic crop, and many loci for important traits have been identified, but it remains challenging and time-consuming to identify candidate or causal genes\/variants and clarify their roles in phenotype formation and regulation. Here, we first collected and integrated the multi-omics datasets including 25 genomes, transcriptomes in 76 tissue samples, epigenome data of five species and metabolome data of 768 metabolites from four tissues, and genetic variation, trait and transcriptome datasets from 4180 cotton accessions. Then, a cotton multi-omics database (CottonMD, http:\/\/yanglab.hzau.edu.cn\/CottonMD\/) was constructed. In CottonMD, multiple statistical methods were applied to identify the associations between variations and phenotypes, and many easy-to-use analysis tools were provided to help researchers quickly acquire the related omics information and perform multi-omics data analysis. Two case studies demonstrated the power of CottonMD for identifying and analyzing the candidate genes, as well as the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.<\/jats:p>","DOI":"10.1093\/nar\/gkac863","type":"journal-article","created":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T20:27:15Z","timestamp":1665433635000},"page":"D1446-D1456","source":"Crossref","is-referenced-by-count":86,"title":["CottonMD: a multi-omics database for cotton biological study"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6283-0753","authenticated-orcid":false,"given":"Zhiquan","family":"Yang","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University , Guangzhou \u00a0510405, China"}]},{"given":"Jing","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"given":"Yiming","family":"Huang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"given":"Shengbo","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"given":"Lulu","family":"Wei","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4732-3950","authenticated-orcid":false,"given":"Dongxu","family":"Liu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"given":"Yonglin","family":"Weng","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"given":"Jinhai","family":"Xiang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"given":"Qiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"}]},{"given":"Zhaoen","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , Anyang \u00a0455000, China"}]},{"given":"Xinhui","family":"Nie","sequence":"additional","affiliation":[{"name":"Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University , Shihezi , Xinjiang \u00a0832000,\u00a0 China"}]},{"given":"Yu","family":"Yu","sequence":"additional","affiliation":[{"name":"Xinjiang Academy of Agricultural and Reclamation Science , Shihezi , Xinjiang \u00a0832000, China"}]},{"given":"Zuoren","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , Anyang \u00a0455000, China"},{"name":"Xinjiang Academy of Agricultural and Reclamation Science , Shihezi , Xinjiang \u00a0832000, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3510-8906","authenticated-orcid":false,"given":"Qing-Yong","family":"Yang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University , Wuhan \u00a0430070, China"},{"name":"Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University , Shihezi , Xinjiang \u00a0832000,\u00a0 China"},{"name":"Xinjiang Academy of Agricultural and Reclamation Science , Shihezi , Xinjiang \u00a0832000, China"}]}],"member":"286","published-online":{"date-parts":[[2022,10,10]]},"reference":[{"key":"2023010804343025800_B1","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1111\/jipb.12076","article-title":"The Gossypiumraimondii genome, a huge leap forward in cotton genomics","volume":"55","author":"Zhu","year":"2013","journal-title":"J. Integr. Plant Biol."},{"key":"2023010804343025800_B2","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/ng.3807","article-title":"Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication","volume":"49","author":"Wang","year":"2017","journal-title":"Nat. Genet."},{"key":"2023010804343025800_B3","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/s41588-018-0116-x","article-title":"Resequencing of 243 diploid cotton accessions based on an updated a genome identifies the genetic basis of key agronomic traits","volume":"50","author":"Du","year":"2018","journal-title":"Nat. Genet."},{"key":"2023010804343025800_B4","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1038\/s41588-018-0119-7","article-title":"Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield","volume":"50","author":"Ma","year":"2018","journal-title":"Nat. Genet."},{"key":"2023010804343025800_B5","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1038\/s41588-021-00844-9","article-title":"The genomic basis of geographic differentiation and fiber improvement in cultivated cotton","volume":"53","author":"He","year":"2021","journal-title":"Nat. Genet."},{"key":"2023010804343025800_B6","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/nbt.3208","article-title":"Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution","volume":"33","author":"Li","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"2023010804343025800_B7","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/nbt.3207","article-title":"Sequencing of allotetraploid cotton (Gossypium hirsutum l. acc. TM-1) provides a resource for fiber improvement","volume":"33","author":"Zhang","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"2023010804343025800_B8","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1038\/s41588-019-0371-5","article-title":"Gossypium barbadense and Gossypiumhirsutum genomes provide insights into the origin and evolution of allotetraploid cotton","volume":"51","author":"Hu","year":"2019","journal-title":"Nat. Genet."},{"key":"2023010804343025800_B9","doi-asserted-by":"crossref","first-page":"3079","DOI":"10.1534\/g3.119.400392","article-title":"De novo genome sequence assemblies of Gossypiumraimondii and Gossypiumturneri","volume":"9","author":"Udall","year":"2019","journal-title":"G3 (Bethesda)"},{"key":"2023010804343025800_B10","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/s41588-020-0614-5","article-title":"Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement","volume":"52","author":"Chen","year":"2020","journal-title":"Nat. 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Adv."},{"key":"2023010804343025800_B14","doi-asserted-by":"crossref","first-page":"D1229","DOI":"10.1093\/nar\/gkt1064","article-title":"CottonGen: a genomics, genetics and breeding database for cotton research","volume":"42","author":"Yu","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023010804343025800_B15","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1186\/s12870-017-1039-x","article-title":"CottonFGD: an integrated functional genomics database for cotton","volume":"17","author":"Zhu","year":"2017","journal-title":"BMC Plant Biol."},{"key":"2023010804343025800_B16","doi-asserted-by":"crossref","first-page":"D1090","DOI":"10.1093\/nar\/gkw910","article-title":"ccNET: database of co-expression networks with functional modules for diploid and polyploid gossypium","volume":"45","author":"You","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023010804343025800_B17","first-page":"D1076","article-title":"MaGenDB: a functional genomics hub for malvaceae plants","volume":"48","author":"Wang","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2023010804343025800_B18","doi-asserted-by":"crossref","first-page":"803736","DOI":"10.3389\/fpls.2021.803736","article-title":"CottonGVD: a comprehensive genomic variation database for cultivated cottons","volume":"12","author":"Peng","year":"2021","journal-title":"Front. Plant Sci."},{"key":"2023010804343025800_B19","doi-asserted-by":"crossref","first-page":"773107","DOI":"10.3389\/fpls.2022.773107","article-title":"GRAND: an integrated genome, transcriptome resources, and gene network database for gossypium","volume":"13","author":"Zhang","year":"2022","journal-title":"Front. Plant Sci."},{"key":"2023010804343025800_B20","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1186\/s12864-016-2662-x","article-title":"Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in china","volume":"17","author":"Nie","year":"2016","journal-title":"BMC Genomics"},{"key":"2023010804343025800_B21","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1007\/s00122-020-03668-z","article-title":"Extensive haplotypes are associated with population differentiation and environmental adaptability in upland cotton (Gossypium hirsutum)","volume":"133","author":"Dai","year":"2020","journal-title":"Thero. Appl. Genet."},{"key":"2023010804343025800_B22","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1038\/s41588-021-00910-2","article-title":"High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement","volume":"53","author":"Ma","year":"2021","journal-title":"Nat. Genet."},{"key":"2023010804343025800_B23","doi-asserted-by":"crossref","first-page":"2070","DOI":"10.3390\/ijms20092070","article-title":"Metabolome and transcriptome association analysis reveals dynamic regulation of purine metabolism and flavonoid synthesis in transdifferentiation during somatic embryogenesis in cotton","volume":"20","author":"Guo","year":"2019","journal-title":"Int. J. Mol. 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