UC Riverside Citrus Genome Project

Overview
Analysis NameUC Riverside Citrus Genome Project
MethodPacBio and Hi-C (assembly with Improved Phased Assembler, annotation BRAKER2)
SourceChandrika Ramadugu
Date performed2023-01-10

CGD Accession: CGD23001

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 australasica CRC3672 genome v1

Taxonomy: Citrus australasica F. Muell. 

Synonyms: Microcitrus australasica (F. Muell.) Swingle; Microcitrus australasica (F. Muell.) Swingle var. australasica 

Cultivar: 'Australian finger lime'  

Accession IDs: IVNO 6502; CRC 3672; PI 312872

The sample was collected from a single tree (inventory identifier IVNO 6502, planted in 1987) in the Givaudan Citrus Variety Collection, University of California Riverside (UCR). The accession is identified as CRC 3672 in the UCR system and PI 312872 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 highly tolerant to the disease (Ramadugu et al., 2016).  This genotype has since been used to breed for HLB resistance in commercial citrus. USDA received this accession as seed in 1966 from L. Chilcott, North Arm Murwillumbah, New South Wales, Australia. It was received at UCR in 1968, most probably as small trees. A clone from this source was propagated and sanitized as VI 697 in 2004 at the Citrus Clonal Protection Program, UCR. 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. 

C. australasica assembly metrics

  Primary Alternate
Number of scaffolds 285 281
Total bases 339,433,343 337,709,420
N50 29,969,644 30,348,868
Assembly BUSCO score (embryophtya_odb10) 99.2% 99.3%
Annotation BUSCO score (embryophyta_odb10) 98.1% 98.1%

 

Citrus glauca CRC3463 genome v1

Taxonomy: Citrus glauca (Lindl.) Burkill 

Synonyms: Eremocitrus glauca (Lindl.) Swingle

Cultivar: 'Australian desert lime'  

Accession IDs:  IVNO 6206; CRC 3463; PI 539717

The sample was collected from a single tree (inventory identifier IVNO 6206, planted in 1983) in the Givaudan Citrus Variety Collection, University of California Riverside (UCR). The accession is identified as CRC 3463 in the UCR system and PI 539717 in the USDA National Plant Germplasm System (NPGS).   Seeds from a related source (Eremocitrus glauca hybrid (Lindl.) Swingle, CRC 4105) 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 highly tolerant to the disease (Ramadugu et al., 2016). In subsequent experiments, C. glauca (CRC 3463) was also found to be highly tolerant to HLB (unpublished). A description of C. glauca 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. glauca assembly metrics

  Primary Alternate
Number of scaffolds 83 83
Total bases 376,481,474 379,226,567
N50 36,986,125 36,716,900
Assembly BUSCO score (embryophtya_odb10) 97.3% 97.4%
Annotation BUSCO score (embryophyta_odb10) 96.1% 95.9%

 

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 3784; PI 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

  Primary Alternate
Number of scaffolds 299 299
Total bases 303,764,154 298,850,376
N50 28,919,117 28,919,117
Assembly BUSCO score (embryophtya_odb10) 97.0% 96.9%
Annotation BUSCO score (embryophyta_odb10) 94.3% 93.8%