Poncirus trifoliata genome v1.3.1 (JGI)

Overview


Analysis Name	Poncirus trifoliata genome v1.3.1 (JGI)
Method	Pacbio, Illumina HiSeq2500, Hi-C (Assembly with Falcon)
Source	JGI-Phytozome, Poncirus trifoliata v1.3.1 (DPI 50-7)
Date performed	2020-11-04

About the assembly

For this genome, please cite Peng et al. 2020. A Chromosome-scale Reference Genome of Trifoliate Orange (Poncirus trifoliata) Provides Insights into Disease Resistance, Cold Tolerance and Genome Evolution in Citrus. 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 PathwayCyc, and view the genome in JBrowse.

Assembly size	265 Mb
Number of scaffolds	152
N50	27,685,527 bp
Predicted transcripts	33,229
Annotated genes	25,537
Assembly BUSCO score (embryophyta_odb10)	98.4%
Annotation BUSCO score (embryophyta_odb10)	98.8%

Downloads

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, P. trifoliata v1.3.1

To download all the original genome assembly and annotation files, please visit the JGI Phytozome website. The files below have been modified by CGD.

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

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: P. trifoliata v1.3.1 Proteins vs. Swissprot
Homology Analysis: P. trifoliata v1.3.1 Proteins vs. TrEMBL

Links