Supporting data for "Sex Chromosome Turnover and Structural Genome Divergence Shapes Meiotic Outcomes in Hybridising <i> Cobitis</i>"

Hybridisation between divergent species can disrupt meiosis and contribute to the emergence of asexual reproduction, yet the genomic mechanisms underlying these outcomes remain insufficiently resolved. In particular, it is unclear whether hybrid sterility and abnormal meiotic behaviour result primarily from genome-wide incompatibilities or from conflicts involving specific chromosomes inherited from the parental species. Similarly, the extent to which hybrids can tolerate differences in sex determination systems, especially under increased ploidy, remains poorly understood. Addressing these questions requires high-quality, chromosome-level reference genomes and complementary cytogenetic resources for the parental species involved in hybrid formation.<br>This project provides chromosome-level genome assemblies for three hybridising loach species of the genus Cobitis (C. elongatoides, C. taenia, and C. tanaitica). The dataset includes genome scaffolding outputs enabling chromosome-scale assemblies, pooled male and female sequencing data (Pool-Seq) supporting population-level analyses of sex-linked differentiation, and molecular cytogenetic resources designed for cross-species chromosome identification. In addition, chromosome-specific painting probes were developed and applied to meiotic metaphase I spreads of diploid hybrids, generating cytogenetic data relevant for assessing chromosome pairing behaviour during meiosis.<br>Together, these resources constitute an integrated genomic and cytogenetic framework for studying hybrid genome architecture, chromosomal structural variation, sex chromosome differentiation, and meiotic chromosome behaviour in a system where hybridisation is linked to sterility and transitions to clonal reproduction. The dataset can be utilised for comparative genomics, investigation of chromosomal rearrangements, identification of sex-linked regions, and cytogenetic analyses of chromosome pairing and segregation in hybrids, as well as for broader research into the evolution of sex determination and reproductive modes in vertebrates.