Genetic Associations with Sex in the Sunflower Sea Star, <i>Pycnopodia helianthoides</i>

Ecological studies of marine invertebrates lacking external sexual dimorphism have often overlooked potential roles of sex and sex determination systems. Yet sex-dependent effects can influence ecological outcomes for many species, including keystone echinoderms like the sunflower sea star (Pycnopodia helianthoides), which can play important roles in maintaining marine biodiversity. Although DNA sequencing has previously been used to document genetic associations with sex in some echinoderms, there is currently little information on sex determination in sea stars lacking sexual dimorphism. Here, we used whole-genome resequencing of 16 female and 18 male P. helianthoides to test for genetic associations with sex and to identify candidate genes. Principal component analysis and outlier tests were used to identify sex-associated genome regions and single-nucleotide polymorphisms distinguishing males from females. We used the annotated P. helianthoides genome to associate gene models with candidate single-nucleotide polymorphisms. Sex-associated single-nucleotide polymorphisms, characterized by male homozygosity and female heterozygosity, were concentrated in distinct haplotypes; the majority (86%) were on just two chromosomes. Of the 76 outlier sex-specific single-nucleotide polymorphisms identified, 73 always discriminated female sea stars from males. These single-nucleotide polymorphisms are in or adjacent to genes involved in gonad formation, sex-specific gene expression, and sex determination processes. These results provide an important resource for identifying sex and enable study of the role that sex plays in the biology, ecology, and conservation of the sunflower sea star.