Homology in Sex Determination in Two Distant Spiny Frogs, Nanorana quadranus and Quasipaa yei

Abstract

Sex determination is remarkably diverse, with frequent transitions between sex chromosomes, in amphibians. Under these transitions, some chromosomes are more likely to be recurrently co-opted as sex chromosomes, as they are often observed across deeply divergent taxa. However, little is known about the pattern of sex chromosome evolution among closely related groups. Here, we examined sex chromosome and sex determination in two spiny frogs, Nanorana quadranus and Quasipaa yei. We conducted an analysis of genotyping-by-sequencing (GBS) data from a total of 34 individuals to identify sex-specific makers, with the results verified by PCR. The results suggest that chromosome 1 is a homologous sex chromosome with an XY pattern in both species. This chromosome has been evolutionarily conserved across these closely related groups within a period of time. The DMRT1 gene is proposed to be implicated in homology across two distantly related spiny frog species as a putative candidate sex-determining gene. Harboring the DMRT1 gene, chromosome 1 would have been independently co-opted for sex determination in deeply divergent groups of anurans.

Keywords: homology; sex chromosome; sex determination.

Figure 1

Gel electrophoresis showing the PCR amplification of markers 22276 (N. quadranus) and 291467 (Q. yei). The locus ID is indicated to the left. ‘M’ indicates a DNA marker. Black arrows indicate the PCR product size.

Figure 2

Mapping of the sex-linked markers of N. quadranus and Q. yei to the reference genome. The sex-linked markers of N. quadranus and Q. yei are mapped to the N. parkeri genome (a,b). The sex-linked markers of N. quadranus and Q. yei are mapped to the Q. spinosa genome (c,d), respectively. The red columns indicate sex chromosomes.

Figure 3

Sex chromosomes and sex-linked genes in four frogs. Sex-determination system and sex-chromosome identities were from GBS data in N. quadranus and Q. yei (the majority of sex-linked markers mapped to chromosome 1 of Q. spinosa and N. parkeri: see detail in Figure S2, Supplementary Tables S4 and S6) and from the literature in R. temporaria and H. arborea [36,47]. Chromosome 1 harbors the candidate gene Dmrt1 for sex determination in four frogs. The dotted lines represent the sex chromosome for each species, and colored dots show sex-linked SNPs in N. quadranus (blue) and Q. yei (red). Sex-linked SNPs are randomly located, and there was no shared XY site found. The grey solid lines show that several sex-linked SNPs were mapped to the Dmrt1 gene. Tree topology and approximate divergence times (My) were adapted using a combination of data from Che et al. (2010), Yuan et al. (2019) [37,48] and http://timetree.org (accessed on 4 February 2024).

Figure 4

The mapping of sex-linked locus of N. quadranus and Q. yei on DMRT1 gene of G. rugosa. Circles indicate sex-linked loci of N. quadranus and Q. yei, and dashed lines indicate the relative alignment region of the DMRT1 gene of G. ruguosa in the reference genome. The blue background sections display the reference genomes utilized for screening sex-linked loci.