{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T06:32:04Z","timestamp":1768631524870,"version":"3.49.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2019YFE0190900"],"award-info":[{"award-number":["2019YFE0190900"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFC2601302"],"award-info":[{"award-number":["2022YFC2601302"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015637","name":"Marine S&T Fund of Shandong Province","doi-asserted-by":"publisher","award":["2022QNLM050101"],"award-info":[{"award-number":["2022QNLM050101"]}],"id":[{"id":"10.13039\/501100015637","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015637","name":"Marine S&T Fund of Shandong Province","doi-asserted-by":"publisher","award":["2022QNLM030005"],"award-info":[{"award-number":["2022QNLM030005"]}],"id":[{"id":"10.13039\/501100015637","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32130107"],"award-info":[{"award-number":["32130107"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871499"],"award-info":[{"award-number":["31871499"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32222085"],"award-info":[{"award-number":["32222085"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key R&D Project of Shandong Province","award":["2021ZLGX03"],"award-info":[{"award-number":["2021ZLGX03"]}]},{"name":"Taishan Scholar Program of Shandong Province, China"}],"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>Evolutionary developmental biology (evo-devo) has been among the most fascinating interdisciplinary fields for decades, which aims to elucidate the origin and evolution of diverse developmental processes. The rapid accumulation of omics data provides unprecedented opportunities to answer many interesting but unresolved evo-devo questions. However, the access and utilization of these resources are hindered by challenges particularly in non-model animals. Here, we establish a comparative multi-omics database for animal evo-devo (EDomics, http:\/\/edomics.qnlm.ac) containing comprehensive genomes, bulk transcriptomes, and single-cell data across 40 representative species, many of which are generally used as model organisms for animal evo-devo study. EDomics provides a systematic view of genomic\/transcriptomic information from various aspects, including genome assembly statistics, gene features and families, transcription factors, transposable elements, and gene expressional profiles\/networks. It also exhibits spatiotemporal gene expression profiles at a single-cell level, such as cell atlas, cell markers, and spatial-map information. Moreover, EDomics provides highly valuable, customized datasets\/resources for evo-devo research, including gene family expansion\/contraction, inferred core gene repertoires, macrosynteny analysis for karyotype evolution, and cell type evolution analysis. EDomics presents a comprehensive and comparative multi-omics platform for animal evo-devo community to decipher the whole history of developmental evolution across the tree of life.<\/jats:p>","DOI":"10.1093\/nar\/gkac944","type":"journal-article","created":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T15:47:13Z","timestamp":1667317633000},"page":"D913-D923","source":"Crossref","is-referenced-by-count":15,"title":["EDomics: a comprehensive and comparative multi-omics database for animal evo-devo"],"prefix":"10.1093","volume":"51","author":[{"given":"Jiankai","family":"Wei","sequence":"first","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Penghui","family":"Liu","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuyun","family":"Liu","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"An","family":"Jiang","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinghan","family":"Qiao","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongqi","family":"Pu","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bingrou","family":"Wang","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongning","family":"Jia","sequence":"additional","affiliation":[{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8112-1730","authenticated-orcid":false,"given":"Yuli","family":"Li","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9571-9864","authenticated-orcid":false,"given":"Shi","family":"Wang","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"},{"name":"Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China , Sanya 572000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1616-5363","authenticated-orcid":false,"given":"Bo","family":"Dong","sequence":"additional","affiliation":[{"name":"Sars-Fang Centre, MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China , Qingdao \u00a0266003, China"},{"name":"Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao \u00a0266237, China"},{"name":"Institute of Evolution & Marine Biodiversity, Ocean University of China , Qingdao \u00a0266003, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,11,1]]},"reference":[{"key":"2023010804285726900_B1","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/35049594","article-title":"Evo-devo: the evolution of a new discipline","volume":"1","author":"Raff","year":"2000","journal-title":"Nat. Rev. Genet."},{"key":"2023010804285726900_B2","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/nrg2062","article-title":"The choice of model organisms in evo-devo","volume":"8","author":"Jenner","year":"2007","journal-title":"Nat. Rev. Genet."},{"key":"2023010804285726900_B3","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/S0169-5347(97)01222-6","article-title":"Phylotypic stage or phantom: is there a highly conserved embryonic stage in vertebrates?","volume":"12","author":"Hall","year":"1997","journal-title":"Trends Ecol. Evol."},{"key":"2023010804285726900_B4","doi-asserted-by":"crossref","DOI":"10.1111\/eva.13456","article-title":"Marine animal evolutionary developmental biology \u2013 advances through technology development","author":"Stracke","year":"2022","journal-title":"Evol. Appl."},{"key":"2023010804285726900_B5","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1007\/s11427-020-1915-y","article-title":"Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms","volume":"64","author":"Zhao","year":"2021","journal-title":"Sci. China-Life Sci."},{"key":"2023010804285726900_B6","doi-asserted-by":"crossref","first-page":"896176","DOI":"10.1155\/2015\/896176","article-title":"Comparative transcriptomes and evo-devo studies depending on next generation sequencing","volume":"2015","author":"Liu","year":"2015","journal-title":"Comput. Math. Method Med."},{"key":"2023010804285726900_B7","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1111\/ede.12336","article-title":"The evo-devo of molluscs: insights from a genomic perspective","volume":"22","author":"Yang","year":"2020","journal-title":"Evol. Dev."},{"key":"2023010804285726900_B8","doi-asserted-by":"crossref","first-page":"2407","DOI":"10.1101\/gad.1365805","article-title":"Surfing with the tunicates into the post-genome era","volume":"19","author":"Satoh","year":"2005","journal-title":"Genes Dev."},{"key":"2023010804285726900_B9","doi-asserted-by":"crossref","first-page":"0120","DOI":"10.1038\/s41559-017-0120","article-title":"Scallop genome provides insights into evolution of bilaterian karyotype and development","volume":"1","author":"Wang","year":"2017","journal-title":"Nat. Ecol. Evol."},{"key":"2023010804285726900_B10","doi-asserted-by":"crossref","first-page":"20220705","DOI":"10.1098\/rspb.2022.0705","article-title":"Echiuran Hox genes provide new insights into the correspondence between Hox subcluster organization and collinearity pattern","volume":"289","author":"Wei","year":"2022","journal-title":"Proc. R. Soc. B"},{"key":"2023010804285726900_B11","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nature25030","article-title":"Convergent evolution of bilaterian nerve cords","volume":"553","author":"Martin-Duran","year":"2018","journal-title":"Nature"},{"key":"2023010804285726900_B12","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41586-019-1290-4","article-title":"Pluripotency and the origin of animal multicellularity","volume":"570","author":"Sogabe","year":"2019","journal-title":"Nature"},{"key":"2023010804285726900_B13","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/s41559-020-1138-1","article-title":"Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae","volume":"4","author":"Wang","year":"2020","journal-title":"Nat. Ecol. Evol."},{"key":"2023010804285726900_B14","doi-asserted-by":"crossref","DOI":"10.1038\/s41559-022-01898-6","article-title":"Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation","author":"Han","year":"2022","journal-title":"Nat. Ecol. Evol."},{"key":"2023010804285726900_B15","first-page":"D668","article-title":"ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates","volume":"48","author":"Dardaillon","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B16","doi-asserted-by":"crossref","first-page":"D970","DOI":"10.1093\/nar\/gkab1005","article-title":"Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms","volume":"50","author":"Arshinoff","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B17","doi-asserted-by":"crossref","first-page":"D988","DOI":"10.1093\/nar\/gkaa918","article-title":"MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca","volume":"49","author":"Liu","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B18","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.ydbio.2016.11.012","article-title":"Independent evolution of genomic characters during major metazoan transitions","volume":"427","author":"Simakov","year":"2017","journal-title":"Dev. Biol."},{"key":"2023010804285726900_B19","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/nrg2311","article-title":"Theodor and Marcella Boveri: chromosomes and cytoplasm in heredity and development","volume":"9","author":"Satzinger","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"2023010804285726900_B20","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nrg2795","article-title":"Next-generation genomics: an integrative approach","volume":"11","author":"Hawkins","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"2023010804285726900_B21","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/j.tree.2010.09.002","article-title":"Adaptation genomics: the next generation","volume":"25","author":"Stapley","year":"2010","journal-title":"Trends Ecol. Evol."},{"key":"2023010804285726900_B22","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkaa1100","article-title":"UniProt: the universal protein knowledgebase in 2021","volume":"49","author":"Bateman","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B23","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B24","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023010804285726900_B25","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The gene ontology resource: 20 years and still GOing strong","volume":"47","author":"Carbon","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B26","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B27","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"2023010804285726900_B28","doi-asserted-by":"crossref","first-page":"D394","DOI":"10.1093\/nar\/gkaa1106","article-title":"PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API","volume":"49","author":"Mi","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804285726900_B29","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s13059-018-1577-z","article-title":"Ten things you should know about transposable elements","volume":"19","author":"Bourque","year":"2018","journal-title":"Genome Biol."},{"key":"2023010804285726900_B30","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/S0959-437X(03)00017-0","article-title":"Evolution of transcription factor function","volume":"13","author":"Hsia","year":"2003","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2023010804285726900_B31","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.cell.2018.01.029","article-title":"The human transcription factors","volume":"172","author":"Lambert","year":"2018","journal-title":"Cell"},{"key":"2023010804285726900_B32","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1093\/molbev\/msp002","article-title":"Gene cluster statistics with gene families","volume":"26","author":"Raghupathy","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"2023010804285726900_B33","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","author":"Skinner","year":"2009","journal-title":"Genome Res"},{"key":"2023010804285726900_B34","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol"},{"key":"2023010804285726900_B35","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2023010804285726900_B36","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1126\/science.1087447","article-title":"A gene-coexpression network for global discovery of conserved genetic modules","volume":"302","author":"Stuart","year":"2003","journal-title":"Science"},{"key":"2023010804285726900_B37","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023010804285726900_B38","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/nmeth.2769","article-title":"The promise of single-cell sequencing","volume":"11","author":"Eberwine","year":"2014","journal-title":"Nat. Methods"},{"key":"2023010804285726900_B39","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.aaf2403","article-title":"Visualization and analysis of gene expression in tissue sections by spatial transcriptomics","volume":"353","author":"Stahl","year":"2016","journal-title":"Science"},{"key":"2023010804285726900_B40","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1038\/s41467-018-03282-0","article-title":"Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor","volume":"9","author":"Crow","year":"2018","journal-title":"Nat. Commun."},{"key":"2023010804285726900_B41","doi-asserted-by":"crossref","first-page":"4325","DOI":"10.1073\/pnas.1720115115","article-title":"Earth biogenome project: sequencing life for the future of life","volume":"115","author":"Lewin","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2023010804285726900_B42","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species","volume":"592","author":"Rhie","year":"2021","journal-title":"Nature"},{"key":"2023010804285726900_B43","first-page":"100264","article-title":"Synergistic engineering of CRISPR-Cas nucleases enables robust mammalian genome editing","volume":"3","author":"Chen","year":"2022","journal-title":"Innovation"},{"key":"2023010804285726900_B44","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1038\/s41586-019-1923-7","article-title":"Improved protein structure prediction using potentials from deep learning","volume":"577","author":"Senior","year":"2020","journal-title":"Nature"},{"key":"2023010804285726900_B45","first-page":"100149","article-title":"Delta.AR: an augmented reality-based visualization platform for 3D genome","volume":"2","author":"Tang","year":"2021","journal-title":"Innovation"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D913\/48441058\/gkac944.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D913\/48441058\/gkac944.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:30:34Z","timestamp":1673152234000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D913\/6786194"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,1]]},"references-count":45,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,11,1]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac944","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,11,1]]}}}