Hippoglossus hippoglossus SNP data for coverage-based sex association

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.