Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)
Cite this dataset
Yang, Xusheng; Luo, Wei; Xia, Yun; Zeng, Xiaomao (2020). Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri) [Dataset]. Dryad. https://doi.org/10.5061/dryad.s4mw6m94b
We use genotyping by sequencing as an approach to identify sex-linked markers in the spiny frog Quasipaa boulengeri with 43 wild-collected adults from a single site. The GBS methodology identified 2 loci on sex differences in allele frequencies, 50 loci on sex differences in heterozygosity, and 523 loci on male-limited occurrence, altogether associated with males heterogamety, indicating an XX-XY system. The sex specificity of five markers was further validated by PCR amplification with a large number of additional individuals from 26 various populations in this species. A total of 27 sex linkage markers were matched to Dmrt1 gene, a ubiquitous role in sex determination and differentiation from flies and nematodes to mammals. Chromosome 1, that harboring Dmrt1, has further been assigned to a highly potential candidate sex chromosome in anurans. Five sex-linked SNP makers explored 3 sex reversals out of 133 individuals here, sparsely showing sex reversal detected in wild amphibian populations.
Genomic DNA of the 43 samples from a single site (DYYEC) was subjected to GBS by the Novogene. Clean Illumina reads were demultiplexed, trimmed, and filtered by the process_radtags function in STACKS [v 2.4]. e used RStudio 1.2.1335 to generate candidate alleles for each individual.
The files generated by the Stacks operation, by changing the parameters M (M controls the number of mismatches allowed between the two alleles of a heterozygote sample), m (m controls the number of identical reads required to initiate a new putative allele) and n (n controls the number of mismatches allowed between any two alleles of the population). Depending on the data set, gapped alignments may provide more loci for the analysis.
Stacks will generate a matches file for each sample through operation comparison. By analyzing these matches files, you can find the depth of each site.
The populations program outputs a summary file for each site of the population. Can be grouped according to needs (such as male and female).
Sex-linked markers were screened with three approaches followed by Brelsford et al. (2017), respectively based on (i) sex differences in allele frequencies, (ii) sex differences in heterozygosity, and (iii) sex-limited occurrence. We used RStudio 1.2.1335 to generate candidate alleles for each individual.
The primer design method was adopted for four sex-linked sites. After amplification in additional samples (10♀10♂) respectively from three populations, the PCR products were sequenced at Sangon Sequencing Center (Shanghai, China).
National Natural Science Foundation of China, Award: NSFC-31772439