2.7 Whole-genome resequencing analyses
The BWA software (version 0.7.10-r789) (Li and Durbin, 2009) was used to
compare high-quality whole-genome resequencing reads with the assembledC. japonica genomes, and reads with low mapping efficiency were
further removed. The parameters were as follows: mem –M –t –K
10000000. Filtered reads in “sam” format was sorted using the Picard
software (https://github.com/broadinstitute/picard) to remove polymerase
chain reaction (PCR) duplication. Single-nucleotide polymorphism (SNP)
and short insertion/deletion (InDel) were called using a Bayesian
approach as implemented in the SAMtools software (Li et al., 2009).
Finally, population differentiation index (F ST)
and genotype frequency were used to locate the sex-determining regions
of C. japonica .