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Citrus Genome Database

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.

Dataset Info

These fields are compatible with DCAT, an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
FieldValue
Authors
Main, Dorrie S.
(ORCID)
Jung, Sook
Product Type
Database
Publisher
MainLab Bioinformatics, Washington State University
Contact Name
Main, Dorrie
Contact Email
Public Access Level
Public
License
Funding Source(s)
National Institute of Food and Agriculture
National Science Foundation
U.S. Department of Agriculture
Washington State University
Modified Date
2018-03-21
Release Date
2018-01-23
Ag Data Commons Keywords: 
  • Genomics & Genetics
  • Genomics & Genetics
  • Genome
  • Genomics & Genetics
  • Sequence Assembly
  • Genomics & Genetics
  • Transcriptome
Program: 
ISO Topic(s):