Citrus sinensis genome v2.0 (HZAU)

Overview
Analysis NameCitrus sinensis genome v2.0 (HZAU)
Methodwhole genome shotgun sequencing, Illumina GAII (Assembly with SOAPdenovo)
SourceHuazhong Ag. Univ.
Date performed2013-01-22

 

About the assembly

For this genome, please cite Xu et al, The draft genome of sweet orange (Citrus sinensis).  This data was originally downloaded from the Citrus sinensis Annotation Project website.  When we added this genome to CGD in 2013, it was given a v2.0 designation.  Please note that this genome corresponds to version 1.0 on the current HZAU website. This genome has been mapped to the genetic map of C. sinensis and is in chromosome scaffolds.  This data is also on NCBI under BioProject PRJNA86123, listed BioSample cultivar designation is Valencia.

Assembly metrics

Assembly size 328 Mb
Number of scaffolds 10
N50 30,837,053 bp
Predicted transcripts 44,275
Annotated genes 29,655
Assembly BUSCO score (embryophyta_odb10)  
Annotation BUSCO score (embryophyta_odb10) 95.6%
Properties
Additional information about this analysis:
Property NameValue
JBrowse URLhttps://www.citrusgenomedb.org/jbrowse/index.html?data=data%2FCsinensis_Hzau_v2.0&loc=
Analysis Typewhole_genome
Download

To download the genome assembly and annotation files, please see 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.