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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #418558
Research Project: Developmental and Environmental Control Mechanisms to Enhance Plant Productivity

Location: Plant Gene Expression Center

Title: Diploid assembly of the Mexican lime genome

Author
item MASSARO, ISABELLE - University Of California Berkeley
item Thomson, James
item Leichty, Aaron

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/9/2025
Publication Date: 9/22/2025
Citation: Massaro, I., Thomson, J.G., Leichty, A.R. 2025. Diploid assembly of the Mexican lime genome. G3: Genes, Genomes, Genetics. 15(11). Article jkaf219. https://doi.org/10.1093/g3journal/jkaf219.
DOI: https://doi.org/10.1093/g3journal/jkaf219

Interpretive Summary: We sequenced the genome of Mexican lime (also known as Key lime), and identify/characterize variation between subgenomes and mosaic variation within clonal varieties. These data will be an important resource for Citrus breeders, and studies of Citrus evolution more generally, and is therefore likely to be of broad interest. Additionally, our analysis of structural variation and the presence of genetic mosaicism will contribute to a growing body of literature documenting this diversity in clonally propagated crops.

Technical Abstract: Clonally propagated crops have long been recognized for their high levels of heterozygosity both between subgenomes within a somatic cell and between cells within an individual clone. Recent developments in long read sequencing technologies have accelerated our ability to identify this diversity and it is increasingly clear that these sources of diversity are abundant in clonal varieties and can contribute to variation in traits of interest to breeders. In this work, we assemble both subgenomes of Mexican lime (Citrus x aurantifolia), an interspecific hybrid between C. hystrix var. micrantha and C. medica. Using this chromosome-level assembly, we find extensive divergence between haplotypes, with at least 89% of the annotated genes harboring polymorphisms at an average rate of 13 per kilobase of coding sequence. Additionally, using high coverage PacBio HiFi libraries from leaf tissue of four individuals we identified multiple large structural variants differing between thorned and thornless lineages, and evidence for mosaicism at hundreds of loci. Many of these variants are found in the promoters and bodies of genes and may act as standing variation for continued improvement of this cultivar.