Citrus australis genome v1.0 (UQ)

Overview
Analysis NameCitrus australis genome v1.0 (UQ)
MethodPacBio CSS, HiFi (Assembly with Hifiasm)
SourceUniversity of Queensland
Date performed2023-04-27

 

CGD Accession: CGD23002

Citation: Upuli Nakandala, Ardashir Kharabian Masouleh, Malcolm W Smith, Agnelo Furtado, Patrick Mason, Lena Constantin, Robert J Henry, Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes, Horticulture Research, 2023; uhad058, https://doi.org/10.1093/hr/uhad058

 

Primary Assembly Metrics

Assembly size 311 Mb
Number of scaffolds 9
N50 36,275,562 bp
Predicted transcripts 32,009
Annotated genes 29,464
Assembly BUSCO score (embryophtya_odb10) 98.9%
Annotation BUSCO score (embryophyta_odb10) 95.4%
Assembly

The Citrus australis Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Citrus_australis_UQ_v1.0.fasta.gz

 

Gene Predictions

The Citrus australis v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Citrus_australis_UQ_v1.0.proteins.fasta.gz
CDS  (FASTA file) Citrus_australis_UQ_v1.0.cds.fasta.gz
Genes (GFF3 file) Citrus_australis_UQ_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Citrus australis Genome v1.0 are available for download below. The Citrus australis Genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan Citrus_australis_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Citrus_australis_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Citrus_australis_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Citrus_australis_v1.0_KEGG-pathways.xlsx.gz

 

Homology

Homology of the Citrus australis Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Citrus australis v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Citrus_australis_v1.0_vs_arabidopsis.xlsx.gz
Citrus australis v1.0 proteins with arabidopsis (Araport11) (FASTA file) Citrus_australis_v1.0_vs_arabidopsis_hit.fasta.gz
Citrus australis v1.0 proteins without arabidopsis (Araport11) (FASTA file) Citrus_australis_v1.0_vs_arabidopsis_noHit.fasta.gz
Citrus australis v1.0 proteins with SwissProt homologs (EXCEL file) Citrus_australis_v1.0_vs_swissprot.xlsx.gz
Citrus australis v1.0 proteins with SwissProt (FASTA file) Citrus_australis_v1.0_vs_swissprot_hit.fasta.gz
Citrus australis v1.0 proteins without SwissProt (FASTA file) Citrus_australis_v1.0_vs_swissprot_noHit.fasta.gz
Citrus australis v1.0 proteins with TrEMBL homologs (EXCEL file) Citrus_australis_v1.0_vs_trembl.xlsx.gz
Citrus australis v1.0 proteins with TrEMBL (FASTA file) Citrus_australis_v1.0_vs_trembl_hit.fasta.gz
Citrus australis v1.0 proteins without TrEMBL (FASTA file) Citrus_australis_v1.0_vs_trembl_noHit.fasta.gz