Sex-associated genomic variation in two ecotypes of Littorina saxatilis on the Swedish west coast

Abstract: Sex, one of the most conspicuous characteristics of living organisms, has always been fascinating for biologists. The diversity of sex goes much beyond a simple distinction between males and females. Many organisms have more than two mating entities, and many species show some degree of hermaphroditism, at least in part of their life cycle. This diversity comes from highly diverse and mostly unknown genetic and environmental factors underlying sex determination. To disentangle the evolution of sex chromosomes, it is required to discover the driving factors of sex-linked loci evolution at the early stages of their emergence. Therefore, species with labile sex chromosome systems showing differing signals for sex-linked regions are more suitable for understanding this complex process. With this purpose in mind, we looked at the difference in sex determination in two ecotypes of Littorina saxatilis on the Swedish west coast. Little is known about the sex-linked genomic regions of L. saxatilis and based on the chromosomal karyotype; there is no ploidy or considerable sex chromosome degeneration. Therefore, it is necessary to use various techniques to verify candidates of sex-associated loci, assuming a pair of homomorphic sex chromosomes. In this study, we utilised an array of reference-based methods, including genomic coverage, SNP density, FST, and GWAS, along with a k-mer reference-free approach. A linkage map was used to place contigs of the reference genome in the correct order. A clear difference has been observed in the sex determination system between Crab and Wave ecotypes. The evidence for sex-associated loci of Crab ecotype was more pronounced and pointed to linkage groups 1, 2 and 12. However, the evidence for sex-linked loci of Wave was much weaker, and none of the linkage groups showed a strong association with sex.