Citrus inodora genome v1.0 (UQ) | Citrus Genome Database

Overview


Analysis Name	Citrus inodora genome v1.0 (UQ)
Method	PacBio CCS (HiFi) (Assembled with Hifiasm v0.19.2-r560)
Source	University of Queensland
Date performed	2024-01-23

CGD Accession: CGD24001

Citation: Nakandala U, Furtado A, Masouleh AK, Smith MW, Mason P, Williams DC, Henry RJ. The genomes of Australian wild limes. Plant molecular biology. 2024 Sep 24; 114(5):102.

Collapsed Assembly Metrics

Assembly size	391 Mb
Number of scaffolds	44
N50	31,512,592 bp
Predicted transcripts	81,747
Annotated genes	72,031
Assembly BUSCO score (embryophtya_odb10)	98.0%
Annotation BUSCO score (embryophyta_odb10)	96.1%

Assembly

The Citrus inodora UQ genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (haplome A)(FASTA file)	Cin-UQ_v1.0.hap1.fasta.gz
Chromosomes (haplome B)(FASTA file)	Cin-UQ_v1.0.hap2.fasta.gz

Gene Predictions

The Citrus inodora UQ v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences (haplome A)(FASTA file)	Cin-UQ_v1.0.hap1.proteins.fasta.gz
CDS (haplome A)(FASTA file)	Cin-UQ_v1.0.hap1.cds.fasta.gz
Genes (haplome A) (GFF3 file)	Cin-UQ_v1.0.hap1.genes.gff3.gz
Protein sequences (haplome B)(FASTA file)	Cin-UQ_v1.0.hap2.proteins.fasta.gz
CDS (haplome B)(FASTA file)	Cin-UQ_v1.0.hap2.cds.fasta.gz
Genes (haplome B) (GFF3 file)	Cin-UQ_v1.0.hap2.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus inodora UQ genome v1.0 are available for download below. The Citrus inodora 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	Cin-UQ_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cin-UQ_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cin-UQ_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cin-UQ_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus inodora UQ 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^-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format.

Protein Homologs

C. inodora UQ v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cin-UQ_v1.0_vs_arabidopsis.xlsx.gz
C. inodora UQ v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cin-UQ_v1.0_vs_arabidopsis_hit.fasta.gz
C. inodora UQ v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cin-UQ_v1.0_vs_arabidopsis_noHit.fasta.gz
C. inodora UQ v1.0 proteins with SwissProt homologs (EXCEL file)	Cin-UQ_v1.0_vs_swissprot.xlsx.gz
C. inodora UQ v1.0 proteins with SwissProt (FASTA file)	Cin-UQ_v1.0_vs_swissprot_hit.fasta.gz
C. inodora UQ v1.0 proteins without SwissProt (FASTA file)	Cin-UQ_v1.0_vs_swissprot_noHit.fasta.gz
C. inodora UQ v1.0 proteins with TrEMBL homologs (EXCEL file)	Cin-UQ_v1.0_vs_trembl.xlsx.gz
C. inodora UQ v1.0 proteins with TrEMBL (FASTA file)	Cin-UQ_v1.0_vs_trembl_hit.fasta.gz
C. inodora UQ v1.0 proteins without TrEMBL (FASTA file)	Cin-UQ_v1.0_vs_trembl_noHit.fasta.gz