Biology subjects

Halenkova, Z.

Publications and source records attributed to Halenkova, Z..

3 recordsLinked to original sources

bioRxiv2026

Stable but turbulent: the two faces of the germline-restricted chromosome of passerine birds

Germline-restricted chromosomes (GRCs) are essential, supernumerary chromosomes that undergo programmed elimination in somatic cells and are only retained in the germline. Despite their recurrent emergence across animals, their genetic composition, function and evolution remain poorly understood. Here we present the most complete and contiguous GRC assemblies, including one nearly telomere-to-telomere GRC assembly, from four closely related passerine bird species, providing an unprecedented insight into the GRCs composition and its evolution over short evolutionary timescales. We show that the passerine GRC is highly enriched in repetitive sequences, with massive, species-specific satellite expansions resulting in enormous differences in GRC size among species. Among mostly recently added sequences, we found only two ancestral genes dating back to the presumed GRC origin, offering clues to its essential function. Importantly, we demonstrate that the GRC undergoes extensive fine-scale within-chromosome rearrangements and copy number changes resulting in little collinearity between species. Our findings indicate that programmed DNA elimination has profoundly changed the GRCs evolution by altering the selection pressures and mutational mechanisms it is exposed to. This makes the GRC an extraordinarily dynamic element in an otherwise stable avian karyotype, retaining core functions while diversifying rapidly, with important implications for germline biology, adaptive evolution and speciation.

evolutionary biology↗

bioRxiv2025

Sex Chromosome Turnover and Structural Interspecific Genome Divergence Shapes Meiotic Outcomes in Hybridizing Cobitis

It has been empirically established that genome mixing between divergent species can trigger meiotic aberrations, ultimately leading to the emergence of asexual reproduction through the production of unreduced gametes in various metazoan lineages. Yet, it remains poorly understood how such asexual hybrids cope with co-inherited differences in sex determination systems, diverged regulatory networks, and chromosomal incompatibilities-- especially 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 to investigate the genetic and cytogenetic basis of hybrid sterility and the transition to asexuality. By integrating genome scaffolding, male/female pooled sequencing, and molecular cytogenetics, we uncover extensive structural variation among homologous chromosomes of the three species, despite their overall syntenic conservation. Population-level Pool-Seq analyses further revealed that each species possesses a distinct, non-homologous sex chromosome, highlighting sex chromosome turnover even among recently diverged lineages. These assemblies enabled 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, with some (e.g., Ch01B) frequently forming bivalents, while others (e.g., Ch01A, Ch05, Ch20) failed to do so and remained unpaired. Our results demonstrate that chromosome-specific features, shaped by structural evolution and sex-linked divergence, contribute unequally to hybrid meiotic failure. Together, this work provides a high-resolution genomic and cytogenetic framework to understand how interspecific hybridization gives rise to clonality, and how the architecture of inherited parental genomes shapes the success or breakdown of meiosis in hybrid vertebrates.

genomics↗

bioRxiv2025

Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes

Centromeres are an important part of chromosomes which direct chromosome segregation during cell division. Their modifications can therefore explain the unusual mitotic and meiotic behaviour of certain chromosomes, such as the germline-restricted chromosome (GRC) of songbirds. This chromosome is eliminated from somatic cells during early embryogenesis and later also from male germ cells during spermatogenesis. Although the mechanism of elimination is not yet known, it is possible that it involves a modification of the centromeric sequence on the GRC, resulting in problems with the attachment of this chromosome to the mitotic or meiotic spindle and its lagging during anaphase, which eventually leads to its elimination from the nucleus. However, the repetitive nature and rapid evolution of centromeres make their identification and comparative analysis across species and chromosomes challenging. Here, we used a combination of cytogenetic and genomic approaches to identify the centromeric sequence of two closely related songbird species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia). We found a 436-bp satellite repeat present in the centromeric regions of all regular chromosomes, making it a strong candidate for the centromeric repeat. This centromeric repeat was highly similar between the two nightingale species. Interestingly, hybridization of the probe to this satellite repeat on meiotic spreads suggested that this repeat is missing on the GRC. Our results indicate that the change of the centromeric sequence may underlie the unusual inheritance and programmed DNA elimination of the GRC in songbirds.

genomics↗