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Citrus Genome Database

posted on 2023-11-30, 08:10 authored by Dorrie S. Main, Sook Jung

The Citrus Genome Database, known as CGD, is a USDA and NSF funded resource to enable basic, translational and applied research in citrus. It houses genomics, genetics and breeding data for citrus species and organisms associated with HLB. It is built by the Mainlab at Washingotn State University using the open-source, generic database platform Tripal.

Although there is wealth of citrus genetic research information, there is still a need for a system that can organize, filter and provide analysis on the available research to be directly applied in breeding programs. The idea of creating this database emerged from several group discussions, in which scientists, breeders, data curators, university professors and bioinformaticians started working on the publicly available genetic and genomic information to make it available for practical use in breeding programs.

The CGD home page allows for quick access to species specific data and popular tools. CGD has tools to view and compare genetic maps, BLAST genomes and reference transcriptomes, JBrowse tool to view genome annotations, and search interfaces to find and download marker, map, QTL and sequence data. Species pages have quick links to data and tools in the sidebar. The MapViewer allows for dynamic visualization of genetic maps.

Available data includes Citrus clementiana genome, Citrus sinensis genomes, Ca. Liberibacter genomes, C. sinensis Reference Transcriptome (RefTrans), 63 Citrus genetic maps, 42,238 Citrus markers, 479 Citrus QTLs, and PathwayCyc for C. clementina and C. sinensis.

Resources in this dataset:


National Institute of Food and Agriculture,

National Science Foundation,

U.S. Department of Agriculture,

Washington State University,


Data contact name

Main, Dorrie

Data contact email


MainLab Bioinformatics, Washington State University


  • Not specified

ISO Topic Category

  • biota

Ag Data Commons Group

  • AgBioData

National Agricultural Library Thesaurus terms

Citrus; genome; databases; USDA; translation (genetics); genomics; breeding; transcriptome; quantitative trait loci; Citrus sinensis; Candidatus Liberibacter

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Main, Dorrie S.; Jung, Sook (2018). Citrus Genome Database. MainLab Bioinformatics, Washington State University.