Citrus inodora CRC3784 genome v1.0
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Overview
CGD Accession: CGD23001 NCBI BioProject Accessions: primary haplotype, PRJNA924048; alternate haplotype, PRJNA924114 Authors: Khushwant Singh, Tara Rickman, Jong-Wong Park, Matthew Huff, Jianyang Liu, Manjunath L. Keremane, Robert R. Krueger, Ping Zheng, Jodi Humann, Madhurababu Kunta, Margaret Staton, Chris Dardick, Mikeal Roose, Dorrie Main, Chandrika Ramadugu. Chromosome-scale, de novo, phased genome assemblies of three Australian limes, Citrus australasica, C. inodora, and C. glauca, towards finding insights into disease resistance to citrus huanglongbing. In preparation. 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, chandram@ucr.edu). 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’
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)
Assembly
The Citrus inodora CRC3784 v1.0 genome v1.0 assembly file is available in FASTA format. Downloads
Gene Predictions
The Citrus inodora CRC3784 v1.0 genome gene prediction files are available in GFF3 and FASTA format. Downloads
Links
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). Downloads
Homology
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
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