Given the economic value and academic significance of lettuce, data accumulation on high-throughput sequencing, phenotyping and other multi-omics has soared, so has the demand for a lettuce integrative database. Here, we launched the LettuceGDB (www.LettuceGDB.com), a comprehensive lettuce database. As an omics data hub, current LettuceGDB integrated two detailed annotated genome references, re-sequencing data over 1,048 lettuce varieties, a collection of more than 1,300 worldwide germplasms and their millions of phenotypic records by manual or through cutting-edge phenomic technologies, re-analyses of 269 RNA-Seq datasets, a complete miRNAome, thousands of metabolites information on representative varieties and wild relatives, epigenetic data on genome-wide chromatin accessibility landscape, and the gallery of lettuce research papers published in the last decade. In order to enable users to access these data conveniently, five hierarchically accessible functions including Genome, Genotype, Germplasm, Phenotype and O-Omics were developed with easy-to-use browsers, search engines, etc. Furthermore, eight built-in tools including Search Gene, Blast, JBrowse, Primer Design, Gene Annotation, Gene Expression, Literature and Download were implemented or deployed for data downloading and browsing, gene functional exploration and experimental practice. Finally, a community forum was established for information sharing, where we systematically summarized the current research progress on different aspects of lettuce. Taken together, we believe LettuceGDB is useful for both scientific research and breeding practices in lettuce, therefore a comprehensive functional database amenable for data mining and database-driven exploration.
Germplasm