Analysis of structural and somatic variation in Mexican lime

Clonally propagated crops have high levels of heterozygosity both between
subgenomes within a somatic cell and between cells within an individual
clone. Recent developments in 2nd and 3rd generation sequencing
technologies have enabled the identification of this diversity, making it
increasingly clear that these sources of diversity are abundant in clonal
varieties and can contribute to variation in traits of interest to
breeders. Compared with citrus cultivars like Sweet Orange, there are
relatively few described accessions for Mexican lime (Citrus x
aurantifolia). Given that many of the described varieties of sweet orange
have been derived from somatic variants, we were interested in examining
this variation in Mexican lime to assess its potential for further
development of this cultivar. Using a recently published diploid assembly
of Mexican lime and 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.