Chromosome-level Genome Assembly of a Norwegian Threespine Stickleback (gasterosteus Aculeatus) Improves Mapping for Ancient DNA and QTL Associated with Parallel Loss of Pelvic Spines.

The threespine stickleback represents a model system for studying parallel evolution, due to the repeated phenotypic adaptation of ancestral marine/anadromous populations to freshwater. Consequently, the genomic architecture underpinning these phenotypic traits has been extensively studied, and an increasing number of genomic resources are available. These include high quality chromosomal reference genome assemblies for Pacific marine and freshwater sticklebacks. However, these reference genomes may bias mapping of short-read data from Atlantic stickleback, and do not fully resolve some repeat-rich regions. Here, we present a chromosome-level reference genome (fGasAcu404) generated from an Atlantic anadromous stickleback using PacBio HiFi and Hi-C data. The assembly improves representation of repeat-rich regions, including on chromosome VII, where the Pitx1 locus and upstream PelA enhancer (Quantitative Trait Loci underpinning repeated loss of the pelvic girdle and spines) are located. Syntenic comparisons and mapping of short reads from well-studied spined and spineless stickleback indicate these loci are incorporated into the new assembly. We evaluate the utility of this reference for paleogenomic analyses by mapping ancient (>10,000 years BP) Norwegian stickleback DNA and assessing inversion karyotypes. We find marginal mapping gains and the ability to robustly infer homozygous ancestral karyotypes at three inversions in two ancient genomes which have predominantly marine-adaptive ancestry. However, karyotype is more ambiguous in an ancient genome with predominantly freshwater ancestry, reflecting the need for further genomic resources for this system. This new reference represents an important step towards the construction of a pangenome that better encompasses genetic variation among ancient and contemporary threespine stickleback populations across their range.