The Citrus Genome Database (CGD, www.citrusgenomedb.org) is a crop community database tailored for citrus researchers and breeders. CGD includes the Breeding Information Management System (BIMS) for both private breeding program management and publicly available phenotype and genotype data. Genetic data include genetic markers, maps, QTL, and GWAS curated from published and integrated with associated data in the database. The data is accessible via several search interfaces. Genetic maps can be viewed through the MapViewer tool, that also visualizes gene and genome data where available. CGD has over 40 genomes of Citrus and other genera in the Rutaceae family. For plant genomes, additional functional annotation and synteny analyses are conducted and made available to search. The genomes can be viewed in JBrowse, sequences searched using BLAST, genome synteny viewed with Synteny Viewer, and metabolic pathways for representative genomes can be viewed and users can overlay -omics data in CitrusCyc. Expression data associated with genes or mRNA of genomes in CGD are also available to view in the Expression Heatmap tool and on the feature page for the corresponding gene/mRNA. Ten bacterial genomes from Ca. Liberibacter and Liberibacter species are also available to search in the database, view in JBrowse, and search the sequences using BLAST. Researchers can also prepare and submit published data to the database using Excel based templates.
