INTRODUCTION: Satellite DNA (satDNA) is a rapidly evolving component of plant genomes, typically found in (peri)centromeric, (sub)telomeric, and other heterochromatic regions. Due to their variability and species- or population-specific distribution, satDNA serves as valuable cytogenetic markers for studying chromosomal rearrangements and karyotype evolution among closely related species. Previous studies have identified species-specific subtelomeric repeats CS-1 in Cannabis sativa, HSR1 in Humulus lupulus, and HJSR in Humulus japonicus. These satellites have been used to differentiate sex chromosomes from autosomes, however, their evolutionary origins, sequence variation and conservation pattern across related species remain largely unexplored. METHODS: In this study, we analyze sequence similarity among these satellites and assess their interspecific chromosomal localization using fluorescence in situ hybridization (FISH). RESULTS: Our results reveal that the HSR1 and HJSR satellites are shared across all studied species, suggesting their common origin from a shared pool of satDNA in their common ancestor. In contrast, the CS-1 satellite exhibits higher sequence divergence. DISCUSSION: Although all three satellites are predominantly localized in subtelomeric regions, we identified species-specific exceptions. These findings provide new insight into the evolutionary dynamics of satDNA within the Cannabaceae family and offer further support for the divergence of Humulus species.

• Klíčová slova
• Humulus, metaphase chromosomes, phylogenetics, satellite divergence, subtelomeric repeats,
• Publikační typ
• časopisecké články MeSH

Sex chromosomes have evolved repeatedly across eukaryotes. The emergence of a sex-determining (SD) locus is expected to progressively restrict recombination, driving convergent molecular differentiation. However, evidence from taxa like teleost fishes, representing over half of vertebrate species with unmatched diversity in SD systems, challenges this model. Teleost sex chromosomes are often difficult to detect as they experience frequent turnovers, resetting the differentiation process. Nothobranchius killifishes, which include the XY system shared by N. furzeri and N. kadleci and X1X2Y systems in six other species, offer a valuable model to study sex chromosome turnovers. We characterised X1X2Y systems in five killifish species and found that sex chromosomes evolved at least four times independently. Sex-determining regions resided near centromeres or predicted chromosome rearrangement breakpoints in N. brieni and N. guentheri, suggesting recombination cold spots may facilitate sex chromosome evolution. Chromosomes representing the XY system in N. furzeri/N. kadleci were sex-linked also in the outgroup Fundulosoma thierryi, with several genes, including gdf6, residing in the region of differentiation. Although the X1X2Y systems of N. guentheri, N. lourensi (both Coastal clade), and N. brieni (Kalahari clade) involved different chromosomes, they shared a potential SD region. We uncovered two sex-linked evolutionary strata of distinct age in N. guentheri. However, its potential SD gene amhr2 was located in the younger stratum and is hence unlikely to be the ancestral SD gene in this lineage. Our findings suggest recombination landscapes shape sex chromosome turnover and that certain synteny blocks are repeatedly co-opted as sex chromosomes in killifishes.

• Klíčová slova
• bacterial artificial chromosome, chromosome fusion, pool‐seq, recombination suppression, sex chromosome differentiation, zoo‐FISH,
• MeSH
• Cyprinodontidae * genetika   MeSH
• fylogeneze MeSH
• molekulární evoluce * MeSH
• pohlavní chromozomy * genetika   MeSH
• procesy určující pohlaví * genetika   MeSH
• rekombinace genetická MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

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 sequences 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 (i.e., autosomes and sex 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.

• Publikační typ
• časopisecké články MeSH

BACKGROUND: Java combtail fish Belontia hasselti (Cuvier, 1831), a member of the Osphronemidae family, inhabits lakes and rivers throughout Southeast Asia and Sri Lanka. Previous cytogenetic research revealed it possesses a diploid chromosome number of 48 chromosomes with a female-heterogametic ZZ/ZW sex chromosome system, where the W chromosome is distinguishable as the only metacentric element in the complement. Female-heterogametic sex chromosome systems seem to be otherwise surprisingly rare in the highly diverse order Perciformes and, therefore, B. hasselti provides an important comparative model to evolutionary studies in this teleost lineage. To examine the level of sex chromosome differentiation in B. hasselti and the contribution of repetitive DNAs to this process we combined bioinformatic analyses with chromosomal mapping of selected repetitive DNA classes, and comparative genomic hybridization. RESULTS: By providing the first satellitome study in Perciformes, we herein identified 13 satellite DNA monomers in B. hasselti, suggesting a very low diversity of satDNA in this fish species. Using fluorescence in situ hybridization, we revealed detectable clusters on chromosomes only for four satellite DNA monomers. Together with the two mapped microsatellite motifs, the repeats primarily accumulated on autosomes, with no distinct clusters located on the sex chromosomes. Comparative genomic hybridization showed no region with accumulated female-specific or enriched repeats on the W chromosome. Telomeric repeats terminated all chromosomes, and no additional interstitial sites were detected. CONCLUSION: These data collectively indicate a low degree of sex chromosome differentiation in B. hasselti despite their considerable heteromorphy. Possible mechanisms that may underlie this pattern are discussed.

• Klíčová slova
• Fishes, Isochromosome, Molecular cytogenetics, Satellitome, Sex chromosome evolution, Teleostei,
• MeSH
• hybridizace in situ fluorescenční MeSH
• mapování chromozomů MeSH
• mikrosatelitní repetice MeSH
• Perciformes * genetika   MeSH
• pohlavní chromozomy * genetika   MeSH
• repetitivní sekvence nukleových kyselin * MeSH
• satelitní DNA genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• satelitní DNA MeSH

Acanthocephalan parasites are often overlooked in many areas of research, and satellitome and cytogenetic analyzes are no exception. The species of the genus Acanthocephalus are known for their very small chromosomes with ambiguous morphology, which makes karyotyping difficult. In this study, we performed the first satellitome analysis of three Acanthocephalus species to identify species- and chromosome-specific satellites that could serve as cytogenetic markers. RepeatExplorer2 revealed a remarkably high number of species-specific repeats, with a predominance of satellite DNAs, alongside variations in repetitive content between sexes. Five satellites in A. anguillae, two in A. lucii and six in A. ranae were successfully mapped to chromosomes using FISH. Each satellite showed a clustered hybridization signal at specific chromosomal locations, which allowed us to create a schematic representation of the distribution of satellites for each species. These newly identified satellites proved to be useful chromosomal markers for the accurate identification of homologous chromosome pairs. No FISH-positive signals were observed on the supernumerary chromosomes of A. anguillae and A. lucii, supporting the hypothesis that these chromosomes have recent origin.

• Klíčová slova
• Acanthocephala, Fluorescence in situ hybridization, Repeat, RepeatExplorer2, Satellite DNA,
• MeSH
• Acanthocephala * genetika   klasifikace   MeSH
• chromozomy genetika   MeSH
• druhová specificita MeSH
• genetické markery MeSH
• hybridizace in situ fluorescenční MeSH
• karyotypizace MeSH
• satelitní DNA * genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• genetické markery MeSH
• satelitní DNA * MeSH

Satellite DNAs (satDNAs) are abundant components of eukaryotic genomes, playing pivotal roles in chromosomal organization, genome stability, and evolution. Here, we combined cytogenetic and genomic methods to characterize the satDNAs in the genomes of Leptidea butterflies. Leptidea is characterized by the presence of a high heterochromatin content, large genomes, and extensive chromosomal reshuffling as well as the occurrence of cryptic species. We show that, in contrast to other Lepidoptera, satDNAs constitute a considerable proportion of Leptidea genomes, ranging between 4.11% and 11.05%. This amplification of satDNAs, together with the hyperactivity of transposable elements, contributes to the substantial genome expansion in Leptidea. Using chromosomal mapping, we show that, particularly LepSat01-100 and LepSat03-167 satDNAs, are preferentially localized in heterochromatin exhibiting variable distribution that may have contributed to the highly diverse karyotypes within the genus. The satDNAs also exhibit W-chromosome accumulation, suggesting their involvement in sex chromosome evolution. Our results provide insights into the dynamics of satDNAs in Lepidoptera genomes and highlight their role in genome expansion and chromosomal organization, which could influence the speciation process. The high proportion of repetitive DNAs in the genomes of Leptidea underscores the complex evolutionary dynamics revealing the interplay between repetitive DNAs and genomic architecture in the genus.

• Klíčová slova
• Lepidoptera, chromosome mapping, cryptic species, genome evolution, repetitive DNA,
• MeSH
• fylogeneze MeSH
• genom hmyzu * MeSH
• heterochromatin genetika   MeSH
• karyotyp * MeSH
• mapování chromozomů MeSH
• molekulární evoluce * MeSH
• motýli * genetika   MeSH
• satelitní DNA * genetika   MeSH
• transpozibilní elementy DNA MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• heterochromatin MeSH
• satelitní DNA * MeSH
• transpozibilní elementy DNA MeSH

Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here, we investigate the evolutionary origin of the previously reported Danaus neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of Tirumala septentrionis (subtribe Danaina), Ideopsis similis (Amaurina), Idea leuconoe (Euploeina) and Lycorea halia (Itunina) and identified their Z-linked scaffolds. We found that the Danaus neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the Melitaea cinxia chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in I. similis and independent fusion occurred between ancestral Z chromosome and McChr12 in L. halia. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analysing the genomic distribution of sex-biased genes in I. leuconoe and L. halia. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both I. leuconoe and L. halia appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z varies across tissues and species.

• Klíčová slova
• butterflies, dosage compensation, fusions, sex chromosomes, sexual antagonism, sex‐biased genes,
• MeSH
• fylogeneze MeSH
• molekulární evoluce MeSH
• motýli * genetika   MeSH
• pohlavní chromozomy * genetika   MeSH
• syntenie MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Repetitive elements can cause large-scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain chromosomal rearrangements that lead to karyotype changes such as fusions and fissions. This is because chromosome segregation during cell division should be less affected than in organisms with a localized centromere. The relationships between repetitive elements and chromosomal rearrangements and how they may translate to patterns of speciation in holocentric organisms are though poorly understood. Here, we use a reference-free approach based on low-coverage short-read sequencing data to characterize the repeat landscape of two independently evolved holocentric groups: Erebia butterflies and Carex sedges. We consider both micro- and macro-evolutionary scales to investigate the repeat landscape differentiation between Erebia populations and the association between repeats and karyotype changes in a phylogenetic framework for both Erebia and Carex. At a micro-evolutionary scale, we found population differentiation in repeat landscape that increases with overall intraspecific genetic differentiation among four Erebia species. At a macro-evolutionary scale, we found indications for an association between repetitive elements and karyotype changes along both Erebia and Carex phylogenies. Altogether, our results suggest that repetitive elements are associated with the level of population differentiation and chromosomal rearrangements in holocentric clades and therefore likely play a role in adaptation and potentially species diversification.

• Klíčová slova
• Carex, Erebia, Lepidoptera, speciation, transposable elements,
• MeSH
• biologická evoluce MeSH
• Carex (rostlina) genetika   MeSH
• fylogeneze * MeSH
• karyotyp * MeSH
• molekulární evoluce MeSH
• motýli * genetika   MeSH
• populační genetika MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• vznik druhů (genetika) MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

In most studied eukaryotes, chromosomes are monocentric, with centromere activity confined to a single region. However, the rush family (Juncaceae) includes species with both monocentric (Juncus) and holocentric (Luzula) chromosomes, where centromere activity is distributed along the entire chromosome length. Here, we combine chromosome-scale genome assembly, epigenetic analysis, immuno-FISH and super-resolution microscopy to study the transition to holocentricity in Luzula sylvatica. We report repeat-based holocentromeres with an irregular distribution of features along the chromosomes. Luzula sylvatica holocentromeres are predominantly associated with two satellite DNA repeats (Lusy1 and Lusy2), while CENH3 also binds satellite-free gene-poor regions. Comparative repeat analysis suggests that Lusy1 plays a crucial role in centromere function across most Luzula species. Furthermore, synteny analysis between L. sylvatica (n = 6) and Juncus effusus (n = 21) suggests that holocentric chromosomes in Luzula could have arisen from chromosome fusions of ancestral monocentric chromosomes, accompanied by the expansion of CENH3-associated satellite repeats.

• MeSH
• centromera * genetika   MeSH
• chromozomy rostlin * genetika   MeSH
• DNA rostlinná genetika   MeSH
• genom rostlinný MeSH
• hybridizace in situ fluorescenční MeSH
• molekulární evoluce MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• satelitní DNA * genetika   MeSH
• syntenie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• satelitní DNA * MeSH

BACKGROUND: The genus Pulmonaria (Boraginaceae) represents a taxonomically complex group of species in which morphological similarity contrasts with striking karyological variation. The presence of different numbers of chromosomes in the diploid state suggests multiple hybridization/polyploidization events followed by chromosome rearrangements (dysploidy). Unfortunately, the phylogenetic relationships and evolution of the genome, have not yet been elucidated. Our study focused on the P. officinalis group, the most widespread species complex, which includes two morphologically similar species that differ in chromosome number, i.e. P. obscura (2n = 14) and P. officinalis (2n = 16). Ornamental cultivars, morphologically similar to P. officinalis (garden escapes), whose origin is unclear, were also studied. Here, we present a pilot study on genome size and repeatome dynamics of these closely related species in order to gain new information on their genome and chromosome structure. RESULTS: Flow cytometry confirmed a significant difference in genome size between P. obscura and P. officinalis, corresponding to the number of chromosomes. Genome-wide repeatome analysis performed on genome skimming data showed that retrotransposons were the most abundant repeat type, with a higher proportion of Ty3/Gypsy elements, mainly represented by the Tekay lineage. Comparative analysis revealed no species-specific retrotransposons or striking differences in their copy number between the species. A new set of chromosome-specific cytogenetic markers, represented by satellite DNAs, showed that the chromosome structure in P. officinalis was more variable compared to that of P. obscura. Comparative karyotyping supported the hybrid origin of putative hybrids with 2n = 15 collected from a mixed population of both species and outlined the origin of ornamental garden escapes, presumably derived from the P. officinalis complex. CONCLUSIONS: Large-scale genome size analysis and repeatome characterization of the two morphologically similar species of the P. officinalis group improved our knowledge of the genome dynamics and differences in the karyotype structure. A new set of chromosome-specific cytogenetic landmarks was identified and used to reveal the origin of putative hybrids and ornamental cultivars morphologically similar to P. officinalis.

• Klíčová slova
• Pulmonaria, Comparative karyotyping, Genome size, Repeatome, Satellite DNA,
• MeSH
• chromozomy rostlin * genetika   MeSH
• délka genomu MeSH
• fylogeneze MeSH
• genom rostlinný * MeSH
• karyotyp MeSH
• karyotypizace * MeSH
• plicník genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH