Citrus clementina genome v1.0 (JGI) | Citrus Genome Database

Overview


Analysis Name	Citrus clementina genome v1.0 (JGI)
Method	whole genome shotgun sequencing, Sanger (Assembly with Arachne)
Source	JGI-Phytozome, Citrus clementina v1.0 (C. x clementina cv. Clemenules, Clementine)
Date performed	2012-12-20

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%

Download

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.

Assembled Scaffolds [FASTA format]
Annotated genes and exons [GFF3 format]
All transcripts [FASTA format]
All CDS [FASTA format]
All proteins [FASTA format]

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.

Homology Analysis: C. clementina v1.0 Proteins vs. Swissprot
Homology Analysis: C. clementina v1.0 Proteins vs. TrEMBL

Links

JBrowse

CitrusCyc