Citrus australasica cv. Rainbow genome v1.0

Overview


Analysis Name	Citrus australasica cv. Rainbow genome v1.0
Method	PacBio Sequel II, Hi-C, Illumina (Assembled with Hifiasm, BWA, Arima, ALSA)
Source	PRJCA019902
Date performed	2024-05-30

About the assembly

For this genome, please cite Nakandala U, Furtado A, Masouleh AK, Smith MW, Williams DC, Henry RJ. The genome of Citrus australasica reveals disease resistance and other species specific genes. BMC plant biology. 2024 Apr 10; 24(1):260. This data was originally downloaded from Genome Warehouse.

Assembly metrics (Hap1 and Hap2 combined)

Assembly size	650 Mb
Number of scaffolds	47
N50	34,174,504 bp
Predicted transcripts	81,160
Annotated genes	72,070
Assembly BUSCO score (embryophyta_odb10)	98.8%
Annotation BUSCO score (embryophyta_odb10)	99.1%

Assembly

The Citrus australasica cv. Rainbow genome v1.0 assembly files are available in FASTA format.

Downloads

Chromosomes (HAP1 FASTA file)	Cau_Rainbow_v1.hap1.fasta.gz
Chromosomes (HAP2 FASTA file)	Cau_Rainbow_v1.hap2.fasta.gz

Gene Predictions

The Citrus australasica cv. Rainbow v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (HAP1 GFF3 file)	Cau_Rainbow_v1.hap1.genes.gff3.gz
Genes (HAP2 GFF3 file)	Cau_Rainbow_v1.hap2.genes.gff3.gz
Protein sequences (HAP1 FASTA file)	Cau_Rainbow_v1.hap1.protein.fasta.gz
Protein sequences (HAP2 FASTA file)	Cau_Rainbow_v1.hap2.protein.fasta.gz
Transcript sequences (HAP1 FASTA file)	Cau_Rainbow_v1.hap1.transcript.fasta.gz
Transcript sequences (HAP2 FASTA file)	Cau_Rainbow_v1.hap2.transcript.fasta.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus australasica cv. Rainbow genome v1.0 are available for download below. The Citrus australasica 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	Cau_Rainbow_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cau_Rainbow_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cau_Rainbow_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cau_Rainbow_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus australasica cv. Rainbow 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. australasica cv. Rainbow v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cau_Rainbow_v1_hap1.0_vs_arabidopsis.xlsx.gz
C. australasica cv. Rainbow v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cau_Rainbow_v1_hap1.0_vs_arabidopsis_hit.fasta.gz
C. australasica cv. Rainbow v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cau_Rainbow_v1_hap1.0_vs_arabidopsis_noHit.fasta.gz
C. australasica cv. Rainbow v1.0 proteins with SwissProt homologs (EXCEL file)	Cau_Rainbow_v1_hap1.0_vs_swissprot.xlsx.gz
C. australasica cv. Rainbow v1.0 proteins with SwissProt (FASTA file)	Cau_Rainbow_v1_hap1.0_vs_swissprot_hit.fasta.gz
C. australasica cv. Rainbow v1.0 proteins without SwissProt (FASTA file)	Cau_Rainbow_v1_hap1.0_vs_swissprot_noHit.fasta.gz
C. australasica cv. Rainbow v1.0 proteins with TrEMBL homologs (EXCEL file)	Cau_Rainbow_v1_hap1.0_vs_trembl.xlsx.gz
C. australasica cv. Rainbow v1.0 proteins with TrEMBL (FASTA file)	Cau_Rainbow_v1_hap1.0_vs_trembl_hit.fasta.gz
C. australasica cv. Rainbow v1.0 proteins without TrEMBL (FASTA file)	Cau_Rainbow_v1_hap1.0_vs_trembl_noHit.fasta.gz