Citrus clementina genome v1.0 (JGI)

Analysis NameCitrus clementina genome v1.0 (JGI)
Methodwhole genome shotgun sequencing, Sanger (Assembly with Arachne)
SourceJGI-Phytozome, Citrus clementina v1.0 (C. x clementina cv. Clemenules, Clementine)
Date performed2012-12-20


About the assembly

Please cite Wu et al. 2014. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication for this genome.  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  301.4 Mb
Number of scaffolds 1,398
N50 31,410,901
Predicted transcripts 33,929
Annotated genes 24,533
Assembly BUSCO score (embryophtya_odb10) 98.6%
Annotation BUSCO score (embryophtya_odb10) 95.6%

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 FTP repository has more files available.

JGI Genome Assembly, C. clementina v1.0:

These files originated from the C. clementina v1.0 genome project page on Phytozyme.

Homology Analysis Results:

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.