A novel amphibian sex determination candidate gene, evolved by structural variation in the regulatory region between X and Y

Abstract

AbstractMost 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 gene is known in >8650 species, thedmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂). Combining a chromosome-scale genome of a non-model amphibian, the European green toad,Bufo(tes)viridis, with ddRAD- and whole genome pool-sequencing revealed a novel candidate master gene (bod1l), governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa and a male long-read assembly uncovered structural X/Y-variation in the 5’-regulatory region, where a Y-specific non-coding RNA, only expressed in males, suggests regional enhancer-properties. Developmental transcriptomes and RNAin-situhybridization provide evidence for timely and spatially relevant, sex-specificbod1l-gene expression in primordial gonads with coinciding differentialH3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a novel mechanism of amphibian sex determination.