Genome Report: Diploid assembly of the Mexican lime genome reveals extensive heterozygosity

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.