Abstract
Many citrus species show high levels of heterozygosity due to their hybrid origin and clonal propagation. This heterozygosity can both hinder and aid efforts to study and improve these cultivars, making it increasingly clear that diploid assemblies have significant advantages over the previous generation of haploid assemblies. In this work, we assemble both subgenomes of Mexican lime (Citrus × aurantifolia), an interspecific hybrid between Citrus hystrix var. micrantha and Citrus medica. The resulting diploid assembly is nearly telomere-to-telomere, spanning 680 Mb. Using subgenome-specific repeats, we were able to phase the 18 chromosomes based on their parent of origin. The resulting hystrix and medica haplotypes show a number of large structural variations, consistent with their distant hybrid ancestry. Despite divergence between haplotypes, syntenic gene pairs were identified for over 90% of the annotated protein coding genes. Within these genes, we find extensive divergence between haplotypes, with at least 89% harboring polymorphisms at an average rate of 13 per kilobase of coding sequence. Knowledge of this variation will be important for future efforts to improve this cultivar using genetic engineering technologies.