Functional dissection and assembly of a small, newly evolved, female-specific genomic region of the W chromosome of the African clawed frog Xenopus laevis

Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small female-specific region of the frog Xenopus laevis that drives female differentiation. Using gene editing, we found that the sex-determining function of this region requires on a gene called dm-w and that the two other female-specific loci (scan-w and ccdc69-w) are not essential for viability, female development, or fertility. Analysis of mesonephros/gonad transcriptomes during sexual differentiation illustrates masculinization of the dm-w knockout transcriptome and identifies mostly non-overlapping sets of differentially expressed genes in three knockout lines (dm-w, scan-w, ccdc69-w) compared to wildtype sisters. Capture sequencing of almost all Xenopus species and PCR surveys indicate that the female-determining function of female-specific region is present in only a subset of species that carry dm-w. These findings map out a dynamic evolutionary history of a newly evolved but functionally fragile female-specific genomic region, whose components have distinctive functions that frequently degraded during Xenopus diversification, and evidence the evolutionary consequences of recombination suppression.