Citrus inodora CRC3784 genome v1.0

Analysis NameCitrus inodora CRC3784 genome v1.0
MethodPacBio Hifi, CCS (Assembly with IPA and Hifiasm)
SourceUniversity of California Riverside
Date performed2023-05-24


CGD Accession: CGD23001

NCBI BioProject Accessions: primary haplotype, PRJNA924048; alternate haplotype, PRJNA924114

Citation:  Singh K, Huff M, Liu J, Park J-W, Rickman T, Keremane M, Krueger RR, Kunta M, Roose ML, Dardick C, et al. Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes: Citrus australasicaC. inodora, and C. glaucaPlants. 2024; 13(11):1460.

Project Information:  The authors have kindly provided this data pre-publication according to the Ft. Lauderdale Accord. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by the authors and/or collaborators of a comprehensive genome analysis such as identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome- scale comparisons with other species.  Bulk download of the assembly files will become available once the data is published.  If you would like access to the data prior to that, please contact the corresponding author directly (Chandrika Ramadugu,

Funding: USDA NIFA  ECDRE #2019-70016-29068 and #2020-70029-33201


Citrus inodora CRC3784 genome v1.0

Taxonomy: Citrus inodora F. M. Bailey
Synonyms: Microcitrus inodora (F. M. Bailey) Swingle 
Cultivar: ‘Large-leaf Australian wild lime’
Accession IDs: IVNO 2781; CRC 3784PI 539741
The sample was collected from a single tree (inventory identifier IVNO 2781, planted in 1993) in the Givaudan Citrus Variety Collection, University of California Riverside (UCR). The accession is identified as CRC 3784 in the UCR system and PI 539741 in the USDA National Plant Germplasm System (NPGS).   Seeds from this source tree were propagated and used for testing for field resistance/tolerance against citrus Huanglongbing (HLB) disease in an HLB endemic region of Florida, USA and found to be tolerant to the disease (Ramadugu et al., 2016).  This genotype has since been used to breed for HLB resistance in commercial citrus. A description of the accession is available here.  Propagative and genetic material from this accession is available from the USDA National Clonal Germplasm Repository for Citrus and Dates, Riverside, California subject to phytosanitary regulations. Note: this accession has not been sanitized.

C. inodora assembly metrics (combined haplotypes)

Number of scaffolds 598
Total bases 602 Mb
N50 28,919,117 b
Assembly BUSCO score (embryophtya_odb10) 96.9%
Annotation BUSCO score (embryophyta_odb10) 89.3%

The Citrus inodora CRC3784 v1.0 genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) cgd_Cinodora_v1.0.fasta.gz
Gene Predictions

The Citrus inodora CRC3784 v1.0 genome gene prediction files are available in GFF3 and FASTA format.


Protein sequences  (FASTA file) cgd_Cinodora_v1.0.proteins.fasta.gz
CDS  (FASTA file) cgd_Cinodora_v1.0.cds.fasta.gz
Genes (GFF3 file) cgd_Cinodora_v1.0.genes.gff3.gz
Functional Analysis

Functional annotation for the Citrus inodora CRC3784 genome v1.0 are available for download below. The Citrus inodora CRC3784 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).


GO assignments from InterProScan cgd_Cinodora_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan cgd_Cinodora_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs cgd_Cinodora_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways cgd_Cinodora_v1.0_KEGG-pathways.xlsx.gz

Homology of the Citrus inodora CRC3784 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 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

C. inodora CRC3784 v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) cgd_Cinodora_v1.0_vs_arabidopsis.xlsx.gz
C. inodora CRC3784 v1.0 proteins with arabidopsis (Araport11) (FASTA file) cgd_Cinodora_v1.0_vs_arabidopsis_hit.fasta.gz
C. inodora CRC3784 v1.0 proteins without arabidopsis (Araport11) (FASTA file) cgd_Cinodora_v1.0_vs_arabidopsis_noHit.fasta.gz
C. inodora CRC3784 v1.0 proteins with SwissProt homologs (EXCEL file) cgd_Cinodora_v1.0_vs_swissprot.xlsx.gz
C. inodora CRC3784 v1.0 proteins with SwissProt (FASTA file) cgd_Cinodora_v1.0_vs_swissprot_hit.fasta.gz
C. inodora CRC3784 v1.0 proteins without SwissProt (FASTA file) cgd_Cinodora_v1.0_vs_swissprot_noHit.fasta.gz
C. inodora CRC3784 v1.0 proteins with TrEMBL homologs (EXCEL file) cgd_Cinodora_v1.0_vs_trembl.xlsx.gz
C. inodora CRC3784 v1.0 proteins with TrEMBL (FASTA file) cgd_Cinodora_v1.0_vs_trembl_hit.fasta.gz
C. inodora CRC3784 v1.0 proteins without TrEMBL (FASTA file) cgd_Cinodora_v1.0_vs_trembl_noHit.fasta.gz