Sex-specific sequence polymorphism in Macquarie perch, but not its three relatives, revealed by amplicon sequencing
For Macquarie perch, genotypes for the ~400-bp region of scaffold 633 captured by amplicon sequencing using F2-R3 primers were consistent with WGS genotypes for the two females and two males from Dartmouth (Appendix G, Table G1). Amplicon sequences for the two individuals from coastal populations (Table G1) showed that only variation at 93229 (the site chosen for the PCR-RFLP sexing assay) might be consistently sex-linked across sequenced individuals. Unique variation at the 146-bp sexing region in two coastal individuals of unknown sex further suggests that sex-linked variation in Macquarie perch could be population-specific. Genotypes for the amplicon-sequenced fragment homologous to the Macquarie perch sex-linked region did not reveal clear sex-linked variation in golden perch (Table G2), Murray cod or trout cod (Table G3).