Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)

catalog.fa.gz, catalog.tags.tsv.gz 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. matches.zip 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. populations.sumstats.tsv The populations program outputs a summary file for each site of the population. Can be grouped according to needs (such as male and female). Quasipaa_ boulengeri_Sex_linked_marker 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. sequences.zip 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).