First version of LettuceGDB online

To better organize all the current data on lettuce in bulk and provide users with friendly interfaces and easy-to-use tools, a comprehensive lettuce genetics and omics database, LettuceGDB (as displayed in the following figure) was constructed, including six assembly genomes representing six genotypes of lettuce: stem lettuce, crisphead lettuce, wild lettuce, losseleaf lettuce, romaine lettuce, and butterhead lettuce. Currently, two reference genomes of stem lettuce and crisphead lettuce with detailed annotations were available to public. In addition, LettuceGDB contains re-sequencing data from over 1000 lettuce varieties; a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies; re-analyses of 256 RNA sequencing datasets; a complete miRNAome; extensive metabolite information for representative varieties and wild relatives; epigenetic data on the genome-wide chromatin accessibility landscape; and various lettuce research papers published in the last decade. Five hierarchically accessible functions (Genome, Genotype, Germplasm, Phenotype, and O-Omics) have been developed with a user-friendly interface to enable convenient data access. Eight built-in tools (Assembly Converter, Search Gene, BLAST, JBrowse, Primer Design, Gene Annotation, Tissue Expression, Literature, and Data) are available for data downloading and browsing, functional gene exploration, and experimental practice.

Figure 1. Framework of three components at LettuceGDB.

LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration, useful for both scientific research and lettuce breeding.

Citation: Guo Z^#, Li B^#, Du J^#, Shen F, Zhao Y, Deng Y, Kuang Z, Tao Y, Wan M, Lu X, Wang D, Wang Y, Han Y, Wei J, Li L, Guo X, Zhao C, Yang X. LettuceGDB: The community database for lettuce genetics and omics. Plant Commun. 2023;4(1):100425. doi:10.1016/j.xplc.2022.100425

Paper available: https://www.sciencedirect.com/science/article/pii/S2590346222002577