Citrus reticulata cv. IRM2 genome v1.0

Overview
Analysis NameCitrus reticulata cv. IRM2 genome v1.0
MethodPacBio Sequel II and Hi-C (Assembly with HiFiasm v0.19.8, Arima, SALSA)
SourceUniversity of Queensland
Date performed2024-06-26

 

CGD Accession: CGD24005

Citation: Nakandala U, Furtado A, Kharabian Masouleh A, Smith MW, Mason P, Henry RJ. Characterizing the structural variations in the genome of the mandarin variety, IrM2, induced by gamma irradiation. Plant biotechnology journal. 2025 Jun 15.

Biosample information: C. reticulata X C. sinensis (Murcott x Ellendale) subjected to gamma irradiation

Assembly Metrics (Hap1 and Hap2 combined)

Assembly size 671 Mb
Number of scaffolds 18
N50 30,547,848 bp
Predicted transcripts 78,851
Annotated genes 69,737
Assembly BUSCO score (embryophtya_odb10) 98.8%
Annotation BUSCO score (embryophyta_odb10) 99.1%
Assembly

The Citrus reticulata cv. IRM2 genome v1.0 assembly files are available in FASTA format.

Downloads

Chromosomes (HAP1 FASTA file) Cr_IRM2_v1.hap1.fasta.gz
Chromosomes (HAP2 FASTA file) Cr_IRM2_v1.hap2.fasta.gz
Gene Predictions

The Citrus reticulata cv. IRM2 v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (HAP1 GFF3 file) Cr_IRM2_v1.hap1.genes.gff3.gz
Genes (HAP2 GFF3 file) Cr_IRM2_v1.hap2.genes.gff3.gz
Protein sequences (HAP1 FASTA file) Cr_IRM2_v1.hap1.protein.fasta.gz
Protein sequences (HAP2 FASTA file) Cr_IRM2_v1.hap2.protein.fasta.gz
CDS (HAP1 FASTA file) Cr_IRM2_v1.hap1.cds.fasta.gz
CDS (HAP2 FASTA file) Cr_IRM2_v1.hap2.cds.fasta.gz
Functional Analysis

Functional annotation for the Citrus reticulata cv. IRM2 genome v1.0 are available for download below. The Citrus reticulata 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 Creticulata_IRM2_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Creticulata_IRM2_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Creticulata_IRM2_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Creticulata_IRM2_v1_KEGG-pathways.xlsx.gz
Homology

Homology of the Citrus reticulata cv. IRM2 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. reticulata cv. IRM2 v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Cr_IRM2_v1_hap1.0_vs_arabidopsis.xlsx
C. reticulata cv. IRM2 v1.0 proteins with arabidopsis (Araport11) (FASTA file) Cr_IRM2_v1_hap1.0_vs_arabidopsis_hit.fasta.gz
C. reticulata cv. IRM2 v1.0 proteins without arabidopsis (Araport11) (FASTA file) Cr_IRM2_v1_hap1.0_vs_arabidopsis_noHit.fasta.gz
C. reticulata cv. IRM2 v1.0 proteins with SwissProt homologs (EXCEL file) Cr_IRM2_v1_hap1.0_vs_swissprot.xlsx
C. reticulata cv. IRM2 v1.0 proteins with SwissProt (FASTA file) Cr_IRM2_v1_hap1.0_vs_swissprot_hit.fasta.gz
C. reticulata cv. IRM2 v1.0 proteins without SwissProt (FASTA file) Cr_IRM2_v1_hap1.0_vs_swissprot_noHit.fasta.gz
C. reticulata cv. IRM2 v1.0 proteins with TrEMBL homologs (EXCEL file) Cr_IRM2_v1_hap1.0_vs_trembl.xlsx
C. reticulata cv. IRM2 v1.0 proteins with TrEMBL (FASTA file) Cr_IRM2_v1_hap1.0_vs_trembl_hit.fasta.gz
C. reticulata cv. IRM2 v1.0 proteins without TrEMBL (FASTA file) Cr_IRM2_v1_hap1.0_vs_trembl_noHit.fasta.gz