{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T04:52:46Z","timestamp":1769921566466,"version":"3.49.0"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T00:00:00Z","timestamp":1634083200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31822052"],"award-info":[{"award-number":["31822052"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Thousand Youth Talents Plan","award":["Z111021502"],"award-info":[{"award-number":["Z111021502"]}]},{"name":"Shaanxi Province Provincial Agricultural","award":["K3370220015"],"award-info":[{"award-number":["K3370220015"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Ruminant Genome Database (RGD; http:\/\/animal.nwsuaf.edu.cn\/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; \u223c8 600 000 conserved elements; and \u223c1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding\u00a0and biomedicine.<\/jats:p>","DOI":"10.1093\/nar\/gkab887","type":"journal-article","created":{"date-parts":[[2021,10,6]],"date-time":"2021-10-06T13:40:43Z","timestamp":1633527643000},"page":"D1091-D1099","source":"Crossref","is-referenced-by-count":50,"title":["RGD v2.0: a major update of the ruminant functional and evolutionary genomics database"],"prefix":"10.1093","volume":"50","author":[{"given":"Weiwei","family":"Fu","sequence":"first","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China"}]},{"given":"Rui","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China"}]},{"given":"Hojjat Asadollahpour","family":"Nanaei","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China"}]},{"given":"Jinxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China"}]},{"given":"Dexiang","family":"Hu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4821-3585","authenticated-orcid":false,"given":"Yu","family":"Jiang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China"},{"name":"Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China"}]}],"member":"286","published-online":{"date-parts":[[2021,10,13]]},"reference":[{"key":"2022010507370789800_B1","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1007\/BF00378733","article-title":"Evolutionary steps of ecophysiological adaptation and diversification of ruminants: a comparative view of their digestive system","volume":"78","author":"Hofmann","year":"1989","journal-title":"Oecologia"},{"key":"2022010507370789800_B2","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.3168\/jds.2009-2071","article-title":"Invited review: ruminant ecology and evolution: perspectives useful to ruminant livestock research and production","volume":"93","author":"Hackmann","year":"2010","journal-title":"J. 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