Citrus sinensis genome v1.1 (JGI)

Analysis NameCitrus sinensis genome v1.1 (JGI)
Methodwhole genome shotgun sequencing, 454 and Sanger (Assembly with Newbler)
SourceJGI-Phytozome, Citrus sinensis v1.1 (Ridge Pineapple, Sweet orange)
Date performed2014-07-01


About the assembly

For this genome, please cite Wu et al. 2014. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.  The original data can be found on the JGI Phytozome website.  Please see the links to the left to download assembly and analysis files, view the pathway cyc, and view the genome in JBrowse.

Assembly metrics

Assembly size  319 Mb
Number of scaffolds 12,574
N50 250,548
Predicted transcripts 46,147
Annotated genes 24,379
Assembly BUSCO score (embryophtya_odb10) 92.2%
Annotation BUSCO score (embryophtya_odb10) 87.5%


The resequencing data that is aligned to the C. clementina v1.0 genome is also available to view in the CGD JBrowse. The BAM and BAI files are available to download on the CGD data repository. The tracks are as below:

Abbreviation Scientific Name Common Name NCBI accession number
CHP Citrus maxima Chandler pummelo SRX372688
CLM Citrus clementina Tanaka clementine mandarin SRX371962
LAP Citrus maxima Low-acid pummelo SRX372702
PKM Citrus reticulata Pokan mandarin SRX372665
SSO Citrus aurantium Seville sour orange SRX372786
SWO Citrus sinensis Ridge Pineapple sweet orange SRX372703
WLM Citrus deliciosa Willowleaf mandarin SRX372685
WMM Citrus reticulata  W. Murcott mandarin SRX372687



Below are links to data files related to this genome assembly.  These files can also be accessed and downloaded from the CGD data repository.  This page has links to the files that are most commonly downloaded.  The CGD data repository has more files available.

JGI Genome Assembly, C. sinensis v1.1:

These files originated from the C. sinensis v1.1 genome project page on Phytozyme.

Homology Analysis:

The protein homolog searches were performed using BLAST (e-value cutoff of 1e-6) and the Swissprot and TrEMBL protein databases by the Main Bioinformatics Lab.  Results were parsed into an Excel format.