{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T03:51:23Z","timestamp":1775447483804,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"vor","delay-in-days":91,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Crop genomics has advanced rapidly during the past decade, which generated a great abundance of omics data from multi-omics studies. How to utilize the accumulating data becomes a critical and urgent demand in crop science. As an attempt to integrate multi-omics data, we developed a database, LettuceDB (https:\/\/db.cngb.org\/lettuce\/), aiming to assemble multidimensional data for cultivated and wild lettuce germplasm. The database includes genome, variome, phenome, microbiome and spatial transcriptome. By integrating user-friendly bioinformatics tools, LettuceDB will serve as a one-stop platform for lettuce research and breeding in the future.<\/jats:p>\n               <jats:p>Database URL: https:\/\/db.cngb.org\/lettuce\/<\/jats:p>","DOI":"10.1093\/database\/baae018","type":"journal-article","created":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T18:21:11Z","timestamp":1711995671000},"source":"Crossref","is-referenced-by-count":10,"title":["LettuceDB: an integrated multi-omics database for cultivated lettuce"],"prefix":"10.1093","volume":"2024","author":[{"given":"Wenhui","family":"Zhou","sequence":"first","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"BGI Research , Wuhan 430074, China"},{"name":"State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research , Shenzhen 518083, China"}]},{"given":"Tao","family":"Yang","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"},{"name":"Guangdong Genomics Data Center, BGl research , Shenzhen 518120, China"}]},{"given":"Liucui","family":"Zeng","sequence":"additional","affiliation":[{"name":"BGI Research , Wuhan 430074, China"},{"name":"South China Agricultural University , Guangzhou 510642, China"}]},{"given":"Jing","family":"Chen","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"}]},{"given":"Yayu","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research , Shenzhen 518083, China"}]},{"given":"Xing","family":"Guo","sequence":"additional","affiliation":[{"name":"BGI Research , Wuhan 430074, China"},{"name":"State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research , Shenzhen 518083, China"}]},{"given":"Lijin","family":"You","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"}]},{"given":"Yiqun","family":"Liu","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"}]},{"given":"Wensi","family":"Du","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"}]},{"given":"Fan","family":"Yang","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"}]},{"given":"Cong","family":"Hua","sequence":"additional","affiliation":[{"name":"BGI Research , Wuhan 430074, China"},{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"}]},{"given":"Jia","family":"Cai","sequence":"additional","affiliation":[{"name":"BGI Research , Wuhan 430074, China"},{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"}]},{"given":"Theo","family":"van Hintum","sequence":"additional","affiliation":[{"name":"Centre for Genetic Resources, the Netherlands , P.O. Box 16, Wageningen 6700 AA, The Netherlands"}]},{"given":"Huan","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research , Shenzhen 518083, China"}]},{"given":"Ying","family":"Gu","sequence":"additional","affiliation":[{"name":"BGI Research , Wuhan 430074, China"},{"name":"State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research , Shenzhen 518083, China"}]},{"given":"Xiaofeng","family":"Wei","sequence":"additional","affiliation":[{"name":"China National GeneBank, BGI Research , Shenzhen 518120, China"},{"name":"Guangdong Genomics Data Center, BGl research , Shenzhen 518120, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2692-7192","authenticated-orcid":false,"given":"Tong","family":"Wei","sequence":"additional","affiliation":[{"name":"BGI Research , Wuhan 430074, China"},{"name":"State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research , Shenzhen 518083, China"}]}],"member":"286","published-online":{"date-parts":[[2024,4,1]]},"reference":[{"key":"2024062912203807500_R1","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/j.tibtech.2004.03.002","article-title":"Plant bioinformatics: from genome to phenome","volume":"22","author":"Edwards","year":"2004","journal-title":"Trends Biotechnol."},{"key":"2024062912203807500_R2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-020-02073-5","article-title":"Sustainable agriculture in the era of omics: knowledge-driven crop breeding","volume":"21","author":"Li","year":"2020","journal-title":"Genome Biol."},{"key":"2024062912203807500_R3","doi-asserted-by":"crossref","DOI":"10.1177\/1177932219899051","article-title":"Multi-omics data integration, interpretation, and its application","volume":"14","author":"Subramanian","year":"2020","journal-title":"Bioinform. Biol. Insights"},{"key":"2024062912203807500_R4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-021-02570-1","article-title":"The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities","volume":"23","author":"Tuggle","year":"2022","journal-title":"Genome Biol."},{"key":"2024062912203807500_R5","doi-asserted-by":"crossref","DOI":"10.1111\/ppl.13672","article-title":"Bioinformatics for plant and agricultural discoveries in the age of multiomics: a review and case study of maize nodal root growth under water deficit","volume":"174","author":"Wang","year":"2022","journal-title":"Physiol. Plant."},{"key":"2024062912203807500_R6","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.tibtech.2010.09.006","article-title":"Making the most of \u2018omics\u2019 for crop breeding","volume":"29","author":"Langridge","year":"2011","journal-title":"Trends Biotechnol."},{"key":"2024062912203807500_R7","article-title":"Applications of multi-omics technologies for crop improvement","volume":"12","author":"Yang","year":"2021","journal-title":"Front. Plant Sci."},{"key":"2024062912203807500_R8","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1016\/j.molp.2023.03.011","article-title":"SoyOmics: a deeply integrated database on soybean multi-omics","volume":"16","author":"Liu","year":"2023","journal-title":"Mol. Plant"},{"key":"2024062912203807500_R9","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/j.molp.2023.03.007","article-title":"BnIR: a multi-omics database with various tools for Brassica napus research and breeding","volume":"16","author":"Yang","year":"2023","journal-title":"Mol. Plant"},{"key":"2024062912203807500_R10","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2020.101241","article-title":"ZEAMAP, a comprehensive database adapted to the maize multi-omics era","volume":"23","author":"Gui","year":"2020","journal-title":"iScience"},{"key":"2024062912203807500_R11","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1111\/j.1601-5223.1960.tb03091.x","article-title":"On the origin of cultivated lettuce","volume":"46","author":"Lindqvist","year":"2010","journal-title":"Hereditas"},{"key":"2024062912203807500_R12","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1023\/A:1008611200727","article-title":"Origin and domestication of Lactuca sativa L","volume":"44","author":"De Vries","year":"1997","journal-title":"Genet. Resour. Crop Evol."},{"key":"2024062912203807500_R13","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14953","article-title":"Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce","volume":"8","author":"Reyes-Chin-Wo","year":"2017","journal-title":"Nat. Commun."},{"key":"2024062912203807500_R14","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-017-02445-9","article-title":"RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis","volume":"8","author":"Zhang","year":"2017","journal-title":"Nat. Commun."},{"key":"2024062912203807500_R15","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/s41588-021-00831-0","article-title":"Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce","volume":"53","author":"Wei","year":"2021","journal-title":"Nat. Genet."},{"key":"2024062912203807500_R16","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2024062912203807500_R17","article-title":"An efficient large-scale whole-genome sequencing analyses practice with an average daily analysis of 100Tbp: ZBOLT","volume":"3","author":"Li","year":"2023","journal-title":"Clin. Transl. Discov."},{"key":"2024062912203807500_R18","volume-title":"Genomics in the Cloud: Using Docker, GATK, and WDL in Terra","author":"Auwera","year":"2020"},{"key":"2024062912203807500_R19","article-title":"GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet","volume":"13","author":"Wang","year":"2022","journal-title":"Nat. Commun."},{"key":"2024062912203807500_R20","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"POPART : full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"2024062912203807500_R21","doi-asserted-by":"crossref","first-page":"33668","DOI":"10.1073\/pnas.2019698117","article-title":"Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce","volume":"117","author":"Yu","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2024062912203807500_R22","article-title":"LettuceGDB: the community database for lettuce genetics and omics","volume":"4(1)","author":"Guo","year":"2023","journal-title":"Plant Commun."},{"key":"2024062912203807500_R23","doi-asserted-by":"crossref","first-page":"10924","DOI":"10.1093\/nar\/gkad840","article-title":"A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants","volume":"51","author":"Wang","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024062912203807500_R24","doi-asserted-by":"crossref","first-page":"D1053","DOI":"10.1093\/nar\/gkad933","article-title":"STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization","volume":"52","author":"Xu","year":"2024","journal-title":"Nucleic Acids Res."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae018\/58365514\/baae018.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae018\/58365514\/baae018.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,29]],"date-time":"2024-06-29T12:30:26Z","timestamp":1719664226000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baae018\/7638744"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,1]]},"references-count":24,"URL":"https:\/\/doi.org\/10.1093\/database\/baae018","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,1,1]]},"published":{"date-parts":[[2024,1,1]]},"article-number":"baae018"}}