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We used annotated genomes and reduced\u2010representation sequencing data for two Australian percichthyids, Macquarie perch <jats:italic>Macquaria australasica<\/jats:italic> and golden perch <jats:italic>M<\/jats:italic>.\u00a0<jats:italic>ambigua<\/jats:italic>, and whole genome resequencing for 50\u00a0Macquarie perch of each sex, to identify sex\u2010linked loci and develop an affordable sexing assay. In silico pool\u2010seq tests of 1,492,004\u00a0Macquarie perch SNPs revealed that a 275\u2010kb scaffold was enriched for gametologous loci. Within this scaffold, 22\u00a0loci were sex\u2010linked in a predominantly XY system, with females being homozygous for the X\u2010linked allele at all 22, and males having the Y\u2010linked allele at &gt;7. Seven XY\u2010gametologous loci (all males, but no females, are heterozygous or homozygous for the male\u2010specific allele) were within a 146\u2010bp region. A PCR\u2010RFLP sexing assay targeting one Y\u2010linked SNP, tested in 66\u00a0known\u2010sex Macquarie perch and two of each sex of three confamilial species, plus amplicon sequencing of 400\u00a0bp encompassing the 146\u2010bp region, revealed that the few sex\u2010linked positions differ between species and between Macquarie perch populations. This indicates sex\u2010chromosome lability in Percichthyidae, supported by nonhomologous scaffolds containing sex\u2010linked loci for Macquarie\u2010 and golden perches. The present resources facilitate genomic research in Percichthyidae, including formulation of hypotheses about candidate genes of interest such as transcription factor <jats:italic>SOX1b<\/jats:italic> that occurs in the 275\u2010kb scaffold ~38\u00a0kb downstream of the 146\u2010bp region containing seven XY\u2010gametologous loci. Sex\u2010linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.<\/jats:p>","DOI":"10.1111\/1755-0998.13569","type":"journal-article","created":{"date-parts":[[2021,12,4]],"date-time":"2021-12-04T15:45:48Z","timestamp":1638632748000},"page":"1639-1655","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Labile sex chromosomes in the Australian freshwater fish family Percichthyidae"],"prefix":"10.1111","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9455-4124","authenticated-orcid":false,"given":"Alexandra","family":"Pavlova","sequence":"first","affiliation":[{"name":"School of Biological Sciences Monash University  Clayton Vic. 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