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Hippoglossus hippoglossus SNP data for coverage-based sex association

Citation

Einfeldt, Anthony; Kess, Tony (2020), Hippoglossus hippoglossus SNP data for coverage-based sex association, Dryad, Dataset, https://doi.org/10.5061/dryad.08kprr50x

Abstract

Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multi-tissue transcriptomes, and population genomic data for the Atlantic Halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged from the Pacific Halibut (Hippoglossus stenolepis), which has a ZZ/ZW system. We used frequency and coverage-based population genomic approaches to identify a putative sex-determining factor, GSDF. We characterized regions with elevated heterozygosity and linkage disequilibrium indicating suppression of recombination across a recently formed sex chromosome. We detected testis-specific expression of GSDF, the sequence for which was highly conserved across flatfish. Based on evidence from genome-wide association, coverage, linkage disequilibrium, testis and brain transcriptomes, and sequence conservation with other flatfish, we propose a mechanism for the recent evolution of an XY sex-determination mechanism in Atlantic Halibut. A loss of function of the ancestral sex-determining gene DMRT1 in regulating the downstream gene GSDF likely enabled GSDF, or a proximal regulatory element, to become the primary sex-determining factor. Our results suggest changes to a small number of elements can have drastic repercussions for the genomic substrate available to sex-specific evolutionary forces, providing insight into how certain elements repeatedly evolve to control sex across taxa. Our chromosome-level assembly, multi-tissue transcriptomes, and population genomic data provide a valuable resource and understanding of the evolution of sexual systems in fishes.

Methods

SNP data were generated from RADseq reduced representation sequencing using the STACKS pipeline.