Labile sex chromosomes in the Australian freshwater fish family Percichthyidae

Pavlova, Alexandra; Harrisson, Katherine; Turakulov, R; Lee, YP; Ingram, BA; Gilligan, D; Sunnucks, P; Gan, HM

doi:10.26181/31021630.v1

Labile sex chromosomes in the Australian freshwater fish family Percichthyidae

https://doi.org/10.26181/31021630

journal contribution

posted on 2026-01-08, 01:26 authored by Alexandra Pavlova, Katherine HarrissonKatherine Harrisson, R Turakulov, YP Lee, BA Ingram, D Gilligan, P Sunnucks, HM Gan

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.

Funding

This work was supported by Australian Research Council Linkage Grants LP110200017 to Monash University, Flinders University and University of Canberra, with Partner Organizations University of Montana, ACTEW Corporation (now Icon Water), Department of Sustainability and Environment (Victoria) (now within Department of Environment, Land, Water & Planning; DELWP), Fisheries Victoria (now within Department of Economic Development, Jobs, Transport and Resources) and Melbourne Water, and LP160100482 to Monash University and La Trobe University, with Partner Organizations University of Canberra, DELWP, Diversity Arrays Technology, Zoos Victoria, Environment, Planning & Sustainable Development Directorate (ACT Government), and Department of Biodiversity, Conservation and Attractions (Western Australia). Sample collection was supported by funding from the Commonwealth Environmental Water Office, Australian Government.

History

Publication Date

2022-05-01

Journal

Molecular Ecology Resources

Volume

22

Issue

4

Pagination

17p. (p. 1639-1655)

Publisher

Wiley

ISSN

1755-098X

Rights Statement

This is the peer reviewed version of the following article: Pavlova A, et al (2022). Labile sex chromosomes in the Australian freshwater fish family Percichthyidae. Molecular Ecology Resources, 22(4), 1639-1655, which has been published in final form at http://doi.org/10.1111/1755-0998.13569. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.