Optical Maps Finish Homologous X and Y Sex Determination Regions in Asparagus

Sex chromosomes in plants are notoriously difficult to assemble. They can contain high densities of repetitive elements, and are often unable to be genetically mapped due to a loss of recombination at sex determination loci. Garden asparagus (Asparagus officinalis) is a unique species to understand how sex chromosomes evolve from autosomes, given that the X and Y chromosomes are cytologically homomorphic and evolutionarily young. Full-length assemblies are necessary to identify all putative sex determination genes and large structural variations between the X and Y chromosomes, but this has proved challenging until recently. Leveraging a doubled haploid YY individual and a doubled haploid mapping population, we generated a chromosome-level genome assembly using Illumina, PacBio, and BioNano optical maps and identified a 1Mb region of non-recombination on the Y chromosome that is largely missing from the X. A single optical map scaffold spanned this entire non-recombining, sex determination region of the Y chromosome. To understand the structure of the X chromosome, we generated a de novo PacBio assembly for a sibling XX female, then hybrid scaffolded the assembly with an additional BioNano optical map. We compared the structure of the X and Y chromosomes and identified a roughly 130kb of X-specific sequence is missing from the homologous region on the Y chromosome. By leveraging BioNano optical maps, we are able to almost fully resolve the structures of the X and Y chromosomes and develop models for the conversion of an autosome into a sex chromosome.