Citrus medica genome v1.0 | Citrus Genome Database

Overview


Analysis Name	Citrus medica genome v1.0
Method	whole genome shotgun, Illumina (Assembly with SOAPdenovo and QUAKE)
Source	Huazhong Ag. Univ.
Date performed	2017-04-10

About the assembly

For this genome, please cite Wang et al, Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. This data was downloaded from the Citrus sinensis Annotation Project website. Please see the links to the left to view the genome in JBrowse. This data is also on NCBI under BioProject PRJNA320023, listed BioSample cultivar designation is XZ.

Assembly metrics

Assembly size	406 Mb
Number of scaffolds	32,732
N50	369,527 bp
Predicted transcripts	47,506
Annotated genes	32,579
Assembly BUSCO score (embryophyta_odb10)	98.5%
Annotation BUSCO score (embryophyta_odb10)	95.5%

Download

To download the genome assembly and annotation files, please visit the CGD data repository.

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.

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

Links

JBrowse

BLAST

CitrusCyc