Database Overview

  • Data Overview 
  • Markers - 3,427 genetic markers consisting of 1514 SNPs, 914 SSRs, 422 RAPD, 246 SRAPs, 88 SCARs, 77 IRAP, 55 Indels,  and the remaining markers are RFLPs, Isozymes, ISSR, CAPs, and STS markers. Marker information includes the germplasm it was identified in and reference where it was first described, and when available and relevant, the DNA library, repeat motif, primers, restriction enzyme, among other information. 
  • Maps 51 linkage maps with 3,334 loci consisting of 50 genetic linkage maps covering all nine chromosomes and 1 association map.
  • QTLs 74 QTL loci from 8 QTL datasets.
  • Genotype 
    Data from 23 measurements using 3 markers for 3 species
  • Species 26 Citrus species with detailed information such as geographic origins, probable hybrid parentage, genome size, etc.
  • Traits -   in development
  • Images -   in development
  • Sequences 181,315 sequences consisting of whole genome sequences (94,438 for Citrus clementina, 46,147 for Citrus sinensis) and 33,846 sequences from NCBI's GenBank.
  • Reference  2,361 references from journal articles, conference proceedings, patents, book chapters, and theses.
  • ESTs - Citrus clementina unigene V1Citrus sinensis unigene V1Citrus trifoliata unigene V1 all built using ESTs downloaded from GenBank (06/22/2010), filtered for quality and contamination and assembled using CAP3 software.
  • Genes 2192 Generic Genes from GenBank sequences, 24,533 CDS data from the Citrus clementina genome v1.0 (JGI)
  • Genomes Citrus clementina genome v1.0 (JGI), Citrus sinensis genome v1.0 (JGI) and Citrus trifoliata v1.0
  • Tools
  • CMap - CMap is a graphical interface  which enables users to view and compare  genetic and physical maps between and among species. Currently there 51 maps in Citrus CMap.
  • GBrowse/JBrowse - GBrowse is a graphical interface that enables users to view genome annotations. Citrus GBrowse currently includes the C. clementina v1.0 (JGI) and C. sinensis v1.0 (JGI) whole genome sequences. JBrowse is GBrowse's successor. 
  • NCBI BLAST finds regions of local similarity between sequences.  BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Datasets available for searching include genome scaffolds, coding regions, peptides and transcripts from the Citrus whole genome sequences and contigs from the unigene assemblies.
  • Batch BLAST runs a wrapper for BLAST, parsing the BLAST output into an Excel file and producing a FASTA file of those sequenes with database homologs.  Users will be notified by email when the job is complete and directed to a website to download the result files.  The same datasets are available in Batch BLAST as the Citrus Genome Database NCBI BLAST.
  • Citrus Cyc can be searched or browsed for metabolic pathways in the C. sinesis and C. clementina databases. It also permits users to overlay experimental results from gene expression or metabolics experiments. 
  • CAP3 assembly server is online tool for assembly of contigs from short sequence reads. If you use the CAP3 software in any published work, please cite: Huang X. and Madan A. (1999) CAP3: A DNA sequence assembly program. Genome Research 9, 868-877.
  • SSR Server allows users to upload a batch of sequences in FASTA format and return information on those sequences that contain microsatellites based on the motif frequency the user specifies. Users will be notified by email when the job is complete and directed to a website to download the result files.  These include an excel file listing  each microsatellite, motif, motif length, motif location in the sequence, whether in an ORF and suggested primers using Primer 3. It also summarizes the motif frequency for the data file uploaded. Alternate primers are also provided in a separate file as are the SSR containing sequences in FASTA format. This feature is in development for the Citrus Genome Database.
  • Search pages
  • Genes search for gene, contig or transcript by name or FASTA sequence, InterPro domain name, Gene Ontology term, KEGG orthologue or pathway. The search can be restricted by Citrus species and data source. 
  • Markers search within or across species, maps, and/or marker types for molecular markers. There is also a search function to find neighboring markers
  • QTLs/MTLs search for QTLs and/or MTLs (simply inherited Mendelian Trait Loci) by any combination of species, trait category, trait name, published symbol or label
  • Publications search all publications related to Citrus genetics, genomics and breeding.

 

Last Updated 1/1/2015