{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T06:00:08Z","timestamp":1780380008520,"version":"3.54.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,10,20]],"date-time":"2020-10-20T00:00:00Z","timestamp":1603152000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Zhengzhou Tobacco Research Institute","award":["110201901024(SJ-03)"],"award-info":[{"award-number":["110201901024(SJ-03)"]}]},{"name":"Zhengzhou Tobacco Research Institute","award":["110202001020(JY-03)"],"award-info":[{"award-number":["110202001020(JY-03)"]}]},{"name":"Zhengzhou Tobacco Research Institute","award":["110201601033(JY-07)"],"award-info":[{"award-number":["110201601033(JY-07)"]}]},{"DOI":"10.13039\/100010097","name":"China Association for Science and Technology","doi-asserted-by":"publisher","award":["2016QNRC001"],"award-info":[{"award-number":["2016QNRC001"]}],"id":[{"id":"10.13039\/100010097","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001381","name":"National Research Foundation of Singapore","doi-asserted-by":"publisher","award":["NRF-RSSS-002"],"award-info":[{"award-number":["NRF-RSSS-002"]}],"id":[{"id":"10.13039\/501100001381","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http:\/\/plncdb.tobaccodb.org\/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five built-in search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.<\/jats:p>","DOI":"10.1093\/nar\/gkaa910","type":"journal-article","created":{"date-parts":[[2020,10,3]],"date-time":"2020-10-03T11:12:38Z","timestamp":1601723558000},"page":"D1489-D1495","source":"Crossref","is-referenced-by-count":143,"title":["PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9683-4402","authenticated-orcid":false,"given":"Jingjing","family":"Jin","sequence":"first","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Lu","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yalong","family":"Xu","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zefeng","family":"Li","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shizhou","family":"Yu","sequence":"additional","affiliation":[{"name":"Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco, Guiyang 550081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Liu","sequence":"additional","affiliation":[{"name":"National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huan","family":"Wang","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nam-Hai","family":"Chua","sequence":"additional","affiliation":[{"name":"Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore"},{"name":"Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9991-423X","authenticated-orcid":false,"given":"Peijian","family":"Cao","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,20]]},"reference":[{"key":"2021010313112155000_B1","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1093\/bioinformatics\/btt107","article-title":"PLncDB: plant long non-coding RNA database","volume":"29","author":"Jin","year":"2013","journal-title":"Bioinformatics"},{"key":"2021010313112155000_B2","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1007\/978-1-4939-9045-0_11","article-title":"Bioinformatics approaches to studying plant long noncoding RNAs (lncRNAs): Identification and functional interpretation of lncRNAs from RNA-Seq data sets","volume":"1933","author":"Sun","year":"2019","journal-title":"Methods Mol. 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