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Overview
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 |
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 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.
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