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

Abstract

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 W chromosome-specific region of the frog Xenopus laevis that contains only three genes (dm-w, scan-w, ccdc69-w) and that drives female differentiation. Using gene editing, we found that the sex-determining function of this region requires dm-w but that 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 separate knockout lines for each of these three W-specific gene compared to wildtype sisters. Capture sequencing of almost all Xenopus species and PCR surveys indicate that the female-determining function of dm-w is present in only a subset of species that carry this gene. These findings map out a dynamic evolutionary history of a newly evolved W chromosome-specific genomic region, whose components have distinctive functions that frequently degraded during Xenopus diversification, and evidence the evolutionary consequences of recombination suppression.

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

“…Notably, to date, in >8740 species of amphibians 18 , the widespread combination of poorly or undifferentiated sex chromosomes with large genome-sizes (see below) have caused a basic knowledge gap with only a single though very well-characterized amphibian master sex-determination gene known in a model species, the African clawed frog ( Xenopus laevis 12 , 19 ) and some related species 20 . The Dm-w gene arose after (and perhaps in response to) tetraploidization, is essential as recently shown in knock-out females 21 , and has been lost secondarily in some tetraploid species 22 .…”

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

“…Sexual development and determination are also diverse in amphibians [34], encompassing female and male heterogamety, unique microscopically recognizable sex chromosomes, and species with undifferentiated sex chromosomes. Sexdetermining genes across these systems are starting to be explored through highthroughput sequencing [6,[35][36][37][38]. For instance, a Y-specific non-coding RNA involved in male sex determination in Bufotes viridis was identified through the application of multiple omics techniques [38].…”