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ARS Home » Pacific West Area » Riverside, California » National Clonal Germplasm Repository for Citrus » Research » Publications at this Location » Publication #415709
Research Project: Citrus and Date Genetic Resource Conservation and Utilization

Location: National Clonal Germplasm Repository for Citrus

Title: 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

Author
item SINGH, K - University Of California, Riverside
item HUFF, M - University Of Tennessee
item LIU, JIANYANG - Oak Ridge Institute For Science And Education (ORISE)
item PARK, JW - Texas A&M University
item RICKMAN, T - University Of Tennessee
item Keremane, Manjunath
item Krueger, Robert
item KUNTA, M - Texas A&M University
item ROOSE, M - University Of California, Riverside
item Dardick, Christopher - Chris
item STATON, M - University Of Tennessee
item RAMADUGU, C - University Of California, Riverside

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2024
Publication Date: 5/24/2024
Citation: Singh, K., Huff, M., Liu, J., Park, J., Rickman, T., Keremane, M.L., Krueger, R., Kunta, M., Roose, M., Dardick, C.D., Staton, M., Ramadugu, C. 2024. 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. Plants. https://doi.org/10.3390/plants13111460.
DOI: https://doi.org/10.3390/plants13111460

Interpretive Summary: Huanglongbing (HLB) is a serious disease of citrus worldwide. Resistance or tolerance to HLB has not been reported in commercial types of citrus. However, wild Australian limes such as Citrus australasica, C. inodora, and C. glauca possess beneficial HLB resistance traits, and have been utilized in a breeding program with the goal of introgressing resistance into progeny produced by hybridization with cultivated citrus. This report documents generation of high-quality de novo genome assemblies of individuals of C. australasica, C. inodora, and C. glauca. Gene annotation studies identified over 25,000 genes in each species, including over 400 R-genes in each species. The high-quality haplotype genomes of wild Australian limes will serve as an important resource to enhance the genetic diversity and utilization of the genetic resources to impart HLB resistance in citrus.

Technical Abstract: Huanglongbing (HLB) is a serious disease of citrus worldwide. Wild Australian limes such as Citrus australasica, C. inodora, and C. glauca possess beneficial HLB resistance traits. Individual trees of the three taxa were extensively used in a breeding program for over a decade to introgress resistance traits in the progeny. We have generated high-quality, phased, de novo genome assem-blies using PacBio long read sequencing. The genome assembly sizes of C. australasica (337 Mb/335 Mb), C. inodora (304 Mb/299 Mb), and C. glauca (376 Mb/379 Mb) were determined for the primary and alternate haplotypes. About 86% to 91% of the genome sequences accounted for the nine chromosome-scale scaffolds. The integrity and completeness of the assembled genomes was estimated to be at 97.2 – 98.8 %. Gene annotation studies identified 25,461 genes in C. australasica, 27,665 in C. inodora and 30,067 in C. glauca. Genes belonging to 118 orthogroups were specific to Australian limes. Analysis of the transcripts showed >71% genes consist of more than one exon. We identified 668 R-genes in C. australasica, 404 in C. inodora, and 564 in C. glauca. In addition, 47 - 56 Phloem protein 2 (PP2) and 20 callose synthase (CalS) genes. The high-quality haplotype genomes of wild Australian limes will serve as an important resource to enhance the genetic diversity and utilization of the genetic resources to impart HLB resistance in citrus.