Synteny search identifies carnivore Y chromosome for evolution of male specific genes

The explosive accumulation of mammalian genomes has provided a valuable resource to characterize the evo­lution of the Y chromosome.Unexpectedly,the Y-chromosome sequence has been characterized in only a small handful of species,with the majority being model organisms.Thus,identification of Y-linked scaffolds from un­ordered genome sequences is becoming more important.Here,we used a syntenic-based approach to generate the scaffolds of the male-specific region of the Y chromosome(MSY)from the genome sequence of 6 male car­nivore species.Our results identified 14,15,9,28,14 and 11 Y-linked scaffolds in polar bears,pacific walruses,red pandas,cheetahs,ferrets and tigers,covering 1.55 Mbp,2.62 Mbp,964 Kb,1.75 Mb,2.17 Mbp and 1.84 Mb MSY,respectively.All the candidate Y-linked scaffolds in 3 selected species(red pandas,polar bears and ti­gers)were successfully verified using polymerase chain reaction.We re-annotated 8 carnivore MSYs including these 6 Y-linked scaffolds and domestic dog and cat MSY;a total of 11 orthologous genes conserved in at least 7 of the 8 carnivores were identified.These 11 Y-linked genes have significantly higher evolutionary rates com­pared with their X-linked counterparts,indicating less purifying selection for MSY genes.Taken together,our study shows that the approach of synteny search is a reliable and easily affordable strategy to identify Y-linked scaffolds from unordered carnivore genomes and provides a preliminary evolutionary study for carnivore MSY genes.