Sex chromosome turnover and structural genome divergence shape meiotic outcomes in hybridizing Cobitis

Hybridization between divergent species can result in meiotic aberrations and the emergence of asexual reproduction. Yet, it remains poorly understood to what extent such outcomes arise from genome-wide incompatibilities versus more specific conflicts among individual chromosomes inherited from parental species, including their ability to pair during meiosis in hybrids. It is also unclear how interspecific hybrids cope with differences in sex determination systems, particularly in the context of increased ploidy. Addressing these questions requires high-quality, chromosome-level reference genomes of the parental species involved in hybrid formation.

Here, we present the first chromosome-level genome assemblies for three hybridizing Cobitis species (C. elongatoides, C. taenia, and C. tanaitica), providing a comprehensive framework for investigating the genomic and cytogenetic basis of hybrid sterility and the transition to asexuality. By integrating genome scaffolding, male/female pooled sequencing (Pool-Seq), and molecular cytogenetics, we uncover extensive structural variation among homologous chromosomes of the three species, despite overall karyotype conservation. Population-level analyses revealed that each species possesses distinct, non-homologous sex chromosomes, highlighting rapid sex chromosome turnover in this recently diverged lineage. Finally, the design of chromosome-specific painting probes, which we applied to meiotic metaphase I spreads of diploid hybrids. This approach revealed striking differences in the pairing success of orthologous chromosomes.

Our results demonstrate that individual orthologous chromosomes differ markedly in their ability to form bivalents during meiosis in hybrids, indicating that hybrid meiotic behaviour is shaped by chromosome-specific incompatibilities rather than uniform genome-wide failure. We also found that even closely related parental species possess distinct, non-homologous sex chromosomes, highlighting rapid turnover of sex determination systems in hybridizing lineages. Together, these findings provide a high-resolution genomic and cytogenetic framework to explore how the architecture of inherited parental genomes influences sex-specific reproductive outcomes in hybrids-ranging from male sterility to the establishment of fertile, clonally reproducing female lineages-and how such asymmetries may contribute to the emergence of asexuality in vertebrates.