A candidate sex determination locus in amphibians, evolved by structural variation between X- and Y-chromosomes

Most vertebrates develop distinct females and males, where sex is determined by repeatedly-evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene is known in >8650 species, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW[female]/ZZ[male]). Combining chromosome-scale female and male genomes of a non- model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing revealed a candidate master locus, governing a male-heterogametic system (XX[female]/XY[male]). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5-regulatory region of the gene bod1l, where a Y-specific non-coding RNA, only expressed in males, suggests that this locus may initiate sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant, sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads with coinciding differential H3K4me- methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.