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Labile sex chromosomes in the Australian freshwater fish family Percichthyidae

Sex‐specific ecology has management implications, but rapid sex‐chromosome turnover in fishes hinders sex‐marker development for monomorphic species. We used annotated genomes and reduced‐representation sequencing data for two Australian percichthyids, Macquarie perch Macquaria australasica and golden perch M. ambigua, and whole genome resequencing for 50 Macquarie perch of each sex, to identify sex‐linked loci and develop an affordable sexing assay. In silico pool‐seq tests of 1,492,004 Macquarie perch SNPs revealed that a 275‐kb scaffold was enriched for gametologous loci. Within this scaffold, 22 loci were sex‐linked in a predominantly XY system, with females being homozygous for the X‐linked allele at all 22, and males having the Y‐linked allele at >7. Seven XY‐gametologous loci (all males, but no females, are heterozygous or homozygous for the male‐specific allele) were within a 146‐bp region. A PCR‐RFLP sexing assay targeting one Y‐linked SNP, tested in 66 known‐sex Macquarie perch and two of each sex of three confamilial species, plus amplicon sequencing of 400 bp encompassing the 146‐bp region, revealed that the few sex‐linked positions differ between species and between Macquarie perch populations. This indicates sex‐chromosome lability in Percichthyidae, supported by nonhomologous scaffolds containing sex‐linked loci for Macquarie‐ and golden perches. The present resources facilitate genomic research in Percichthyidae, including formulation of hypotheses about candidate genes of interest such as transcription factor SOX1b that occurs in the 275‐kb scaffold ~38 kb downstream of the 146‐bp region containing seven XY‐gametologous loci. Sex‐linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.