{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T10:10:32Z","timestamp":1780395032181,"version":"3.54.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,9,27]],"date-time":"2019-09-27T00:00:00Z","timestamp":1569542400000},"content-version":"vor","delay-in-days":269,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"NationalNatural Science Foundation of China","doi-asserted-by":"publisher","award":["9143511\/31401453"],"award-info":[{"award-number":["9143511\/31401453"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LZ17C130001"],"award-info":[{"award-number":["LZ17C130001"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Central Universities of China","award":["2017QNA6013"],"award-info":[{"award-number":["2017QNA6013"]}]},{"DOI":"10.13039\/501100013314","name":"National 111 Project of China","doi-asserted-by":"publisher","award":["B17039"],"award-info":[{"award-number":["B17039"]}],"id":[{"id":"10.13039\/501100013314","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2017 M612002"],"award-info":[{"award-number":["2017 M612002"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jiangsu Collaborative Innovation Center for Modern Crop Production"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice genomic databases have been constructed, a database providing large-scale curated genomic data from rice relatives and offering specific gene resources is still lacking. Here, we present RiceRelativesGD, a user-friendly genomic database of rice relatives. RiceRelativesGD integrates large-scale genomic resources from 2 cultivated rice and 11 rice relatives, including 208\u2009321 specific genes and 13\u2009643 genes related to photosynthesis and responsive to external stimuli. Diverse bioinformatics tools are embedded in the database, which allow users to search, visualize and download the information of interest. To our knowledge, this is the first genomic database providing a centralized genetic resource of rice relatives. RiceRelativesGD will serve as a significant and comprehensive knowledgebase for the rice community.<\/jats:p>","DOI":"10.1093\/database\/baz110","type":"journal-article","created":{"date-parts":[[2019,8,17]],"date-time":"2019-08-17T19:12:11Z","timestamp":1566069131000},"source":"Crossref","is-referenced-by-count":14,"title":["RiceRelativesGD: a genomic database of rice relatives for rice research"],"prefix":"10.1093","volume":"2019","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5021-8628","authenticated-orcid":false,"given":"Lingfeng","family":"Mao","sequence":"first","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"},{"name":"Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meihong","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinjie","family":"Chu","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Jia","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"},{"name":"Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Most Humaira","family":"Sultana","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongya","family":"Wu","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangdong","family":"Kong","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Qiu","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chu-Yu","family":"Ye","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"},{"name":"Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian-Hao","family":"Zhu","sequence":"additional","affiliation":[{"name":"CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"},{"name":"Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longjiang","family":"Fan","sequence":"additional","affiliation":[{"name":"Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China"},{"name":"Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,9,27]]},"reference":[{"key":"2019092705515721800_ref1","doi-asserted-by":"crossref","first-page":"E4954","DOI":"10.1073\/pnas.1418307111","article-title":"Rapid diversification of five Oryza AA genomes associated with rice adaptation","volume":"111","author":"Zhang","year":"2014","journal-title":"Proc. Natl. Acad. Sci."},{"key":"2019092705515721800_ref2","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/1471-2164-11-121","article-title":"Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis","volume":"11","author":"Sakai","year":"2010","journal-title":"BMC Genomics"},{"key":"2019092705515721800_ref3","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1104\/pp.113.217497","article-title":"Coordination of leaf photosynthesis, transpiration, and structural traits in rice and wild relatives (genus Oryza)","volume":"162","author":"Giuliani","year":"2013","journal-title":"Plant Physiol."},{"key":"2019092705515721800_ref4","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1270\/jsbbs.60.518","article-title":"The species of the genus Oryza and transfer of useful genes from wild species into cultivated rice, O. sativa","volume":"60","author":"Jena","year":"2010","journal-title":"Breed. Sci."},{"key":"2019092705515721800_ref5","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1016\/j.tplants.2018.09.009","article-title":"Genomic clues for crop\u2013weed interactions and evolution","volume":"23","author":"Guo","year":"2018","journal-title":"Trends Plant Sci."},{"key":"2019092705515721800_ref6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s12284-009-9022-2","article-title":"The evolutionary history of Ehrhartoideae, Oryzeae, and Oryza","volume":"2","author":"Kellogg","year":"2009","journal-title":"Rice"},{"key":"2019092705515721800_ref7","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1038\/s41467-017-01067-5","article-title":"Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed","volume":"8","author":"Guo","year":"2017","journal-title":"Nat. Commun."},{"key":"2019092705515721800_ref8","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1038\/ng.695","article-title":"Genome-wide asociation studies of 14 agronomic traits in rice landraces","volume":"42","author":"Huang","year":"2010","journal-title":"Nat. Genet."},{"key":"2019092705515721800_ref9","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/ng.1018","article-title":"Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm","volume":"44","author":"Huang","year":"2012","journal-title":"Nat. Genet."},{"key":"2019092705515721800_ref10","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1038\/nature19760","article-title":"Genomic architecture of heterosis for yield traits in rice","volume":"537","author":"Huang","year":"2016","journal-title":"Nature"},{"key":"2019092705515721800_ref11","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1038\/ng.3596","article-title":"Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice","volume":"48","author":"Yano","year":"2016","journal-title":"Nat. Genet."},{"key":"2019092705515721800_ref12","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1038\/s41588-018-0041-z","article-title":"Pan-genome analysis highlihgts the extent of genomic variation in cultivated and wild rice","volume":"50","author":"Zhao","year":"2018","journal-title":"Nat. Genet."},{"key":"2019092705515721800_ref13","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1126\/science.1068037","article-title":"A draft sequence of the rice genome (Oryza sativa L. ssp. indica)","volume":"296","author":"Yu","year":"2002","journal-title":"Science"},{"key":"2019092705515721800_ref14","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.1068275","article-title":"A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)","volume":"296","author":"Goff","year":"2002","journal-title":"Science"},{"key":"2019092705515721800_ref15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1939-8433-6-4","article-title":"Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data","volume":"6","author":"Kawahara","year":"2013","journal-title":"Rice"},{"key":"2019092705515721800_ref16","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1038\/ncomms2596","article-title":"Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution","volume":"4","author":"Chen","year":"2013","journal-title":"Nat. Commun."},{"key":"2019092705515721800_ref17","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1038\/ng.3044","article-title":"The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication","volume":"46","author":"Wang","year":"2014","journal-title":"Nat. Genet."},{"key":"2019092705515721800_ref18","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1111\/tpj.12912","article-title":"A host plant genome (Zizania latifolia) after a century-long endophyte infection","volume":"83","author":"Guo","year":"2015","journal-title":"Plant J."},{"key":"2019092705515721800_ref19","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms15324","article-title":"Sequencing and de novo assembly of a near complete indica rice genome","volume":"8","author":"Du","year":"2017","journal-title":"Nat. Commun."},{"key":"2019092705515721800_ref20","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41588-018-0040-0","article-title":"Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza","volume":"50","author":"Stein","year":"2018","journal-title":"Nat. Genet."},{"key":"2019092705515721800_ref21","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1093\/molbev\/msx116","article-title":"TimeTree: a resource for timelines, Timetrees, and divergence times","volume":"34","author":"Kumar","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"2019092705515721800_ref22","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1939-8433-6-4","article-title":"Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data","volume":"6","author":"Kawahara","year":"2013","journal-title":"Rice"},{"key":"2019092705515721800_ref23","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1016\/j.cub.2018.05.066","article-title":"The rise and fall of African rice cultivation revealed by analysis of 246 new genomes","volume":"28","author":"Cubry","year":"2018","journal-title":"Curr. Biol."},{"key":"2019092705515721800_ref24","doi-asserted-by":"crossref","first-page":"e6","DOI":"10.1093\/pcp\/pcs183","article-title":"Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics","volume":"54","author":"Sakai","year":"2013","journal-title":"Plant Cell Physiol."},{"key":"2019092705515721800_ref25","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/j.molp.2017.10.003","article-title":"Rice information GateWay: a comprehensive bioinformatics platform for Indica rice genomes","volume":"11","author":"Song","year":"2018","journal-title":"Mol. Plant"},{"key":"2019092705515721800_ref26","doi-asserted-by":"crossref","first-page":"D377","DOI":"10.1093\/nar\/gkh085","article-title":"BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics","volume":"32","author":"Zhao","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2019092705515721800_ref27","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1093\/nar\/gkw958","article-title":"RPAN: rice pan-genome browser for \u223c3000 rice genomes","volume":"45","author":"Sun","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019092705515721800_ref28","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.cpb.2016.12.003","article-title":"SNP-seek II: a resource for allele mining and analysis of big genomic data in Oryza sativa","volume":"7\u20138","author":"Mansueto","year":"2016","journal-title":"Curr. Plant Biol."},{"key":"2019092705515721800_ref29","doi-asserted-by":"crossref","first-page":"D1018","DOI":"10.1093\/nar\/gku894","article-title":"RiceVarMap: a comprehensive database of rice genomic variations","volume":"43","author":"Zhao","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019092705515721800_ref30","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/pcp\/pcv171","article-title":"OryzaGenome: genome diversity database of wild Oryza species","volume":"57","author":"Ohyanagi","year":"2016","journal-title":"Plant Cell Physiol."},{"key":"2019092705515721800_ref31","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1270\/jsbbs.60.544","article-title":"Oryzabase: an integrated information resource for rice science","volume":"60","author":"Yamazaki","year":"2010","journal-title":"Breed. Sci."},{"key":"2019092705515721800_ref32","doi-asserted-by":"crossref","first-page":"D1172","DOI":"10.1093\/nar\/gkv1141","article-title":"Information commons for Rice (IC4R)","volume":"44","author":"Zhang","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019092705515721800_ref33","doi-asserted-by":"crossref","first-page":"D1181","DOI":"10.1093\/nar\/gkx1111","article-title":"Gramene 2018: unifying comparative genomics and pathway resources for plant research","volume":"46","author":"Tello-Ruiz","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019092705515721800_ref34","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol."},{"key":"2019092705515721800_ref35","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":"2019092705515721800_ref36","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1111\/pce.12231","article-title":"Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data","volume":"37","author":"Lohse","year":"2014","journal-title":"Plant Cell Environ."},{"key":"2019092705515721800_ref37","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information","volume":"43","author":"Bateman","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019092705515721800_ref38","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2019092705515721800_ref39","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-28948-z","article-title":"GOATOOLS: a python library for gene ontology analyses","volume":"8","author":"Klopfenstein","year":"2018","journal-title":"Sci. Rep."},{"key":"2019092705515721800_ref40","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2019092705515721800_ref41","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 - approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"2019092705515721800_ref42","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"2019092705515721800_ref43","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":"2019092705515721800_ref44","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":"2019092705515721800_ref45","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1093\/bioinformatics\/btx324","article-title":"PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization","volume":"33","author":"Kreft","year":"2017","journal-title":"Bioinformatics"},{"key":"2019092705515721800_ref46","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/nature03895","article-title":"The map-based sequence of the rice genome","volume":"436","author":"Matsumoto","year":"2005","journal-title":"Nature"},{"key":"2019092705515721800_ref47","first-page":"908","article-title":"Deleterious variants in Asian Rice and the potential cost of domestication","volume":"34","author":"Liu","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"2019092705515721800_ref48","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41559-019-0822-5","article-title":"Rapid evolution of protein diversity by de novo origination in Oryza","volume":"3","author":"Zhang","year":"2019","journal-title":"Nat. Ecol. Evol."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baz110\/30064950\/baz110.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,27]],"date-time":"2019-09-27T09:52:45Z","timestamp":1569577965000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baz110\/5574892"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,1]]},"references-count":48,"URL":"https:\/\/doi.org\/10.1093\/database\/baz110","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019]]},"published":{"date-parts":[[2019,1,1]]},"article-number":"baz110"}}