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

Overview


Analysis Name	Citrus glauca genome v1.0 (UQ)
Method	Pacbio CCS (Hifi) (Assembly with Hifiasm v0.19.2-r560)
Source	University of Queensland
Date performed	2024-01-23

CGD Accession: CGD24002

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	340 Mb
Number of scaffolds	17
N50	33,467,929 bp
Predicted transcripts	74,153
Annotated genes	64,703
Assembly BUSCO score (embryophtya_odb10)	97.0%
Annotation BUSCO score (embryophyta_odb10)	96.8%

Assembly

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

Downloads

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

Gene Predictions

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

Downloads

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

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus glauca UQ genome v1.0 are available for download below. The Citrus glauca 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	Cg_UQ_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cg_UQ_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cg_UQ_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cg_UQ_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus glauca 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. glauca UQ v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cg_UQ_v1.0_vs_arabidopsis.xlsx.gz
C. glauca UQ v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cg_UQ_v1.0_vs_arabidopsis_hit.fasta.gz
C. glauca UQ v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cg_UQ_v1.0_vs_arabidopsis_noHit.fasta.gz
C. glauca UQ v1.0 proteins with SwissProt homologs (EXCEL file)	Cg_UQ_v1.0_vs_swissprot.xlsx.gz
C. glauca UQ v1.0 proteins with SwissProt (FASTA file)	Cg_UQ_v1.0_vs_swissprot_hit.fasta.gz
C. glauca UQ v1.0 proteins without SwissProt (FASTA file)	Cg_UQ_v1.0_vs_swissprot_noHit.fasta.gz
C. glauca UQ v1.0 proteins with TrEMBL homologs (EXCEL file)	Cg_UQ_v1.0_vs_trembl.xlsx.gz
C. glauca UQ v1.0 proteins with TrEMBL (FASTA file)	Cg_UQ_v1.0_vs_trembl_hit.fasta.gz
C. glauca UQ v1.0 proteins without TrEMBL (FASTA file)	Cg_UQ_v1.0_vs_trembl_noHit.fasta.gz