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PubMed2026

Satellite DNAs in Drosophila koepferae (repleta group) reveal patterns of origin, chromosomal organization, transcription, and turnover in the buzzatii cluster.

Satellite DNAs (satDNAs) are non-coding tandem repeats that can comprise more than 20% of eukaryotic genomes. They contribute to structural and regulatory processes in the genome and often evolve rapidly, shaping early stages of genetic differentiation between populations and species. Although Drosophila has long served as a model for studying satDNA biology, little is known about satDNAs in non-model Drosophila species, particularly within the repleta group, one of the most species-rich lineages in the genus. To reduce such bias, several studies have focused on the buzzatii cluster (repleta group). However, D. koepferae remained the only species lacking comprehensive satDNA data, limiting comparative analyses. Here, we used publicly available genomic sequencing data from two D. koepferae populations (Argentina and Bolivia) to characterize their satDNA content. Both populations share the same set of five satDNAs (CDSTR8, CDSTR138, CDSTR230, DBC-150 and CDSTR177), which together account for ~ 0,9% of the genomic DNA. We show that CDSTR177 originated through amplification of an internal segment of the Galileo transposable element, an event restricted to D. koepferae. All satDNAs localize to heterochromatic regions, with CDSTR138 most likely associated to the centromeres of most chromosomes. Transcripts from all satDNAs were detected, although at low levels. Our results provide new insights into the origin, genomic contribution, expression and evolution of satDNAs in the buzzatii cluster, support incipient differentiation between Argentinean and Bolivian populations of D. koepferae and contribute to clarifying the phylogenetic position of this species within the buzzatii cluster.

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PubMed2026

Satellite DNA evolution in Tytonidae (Aves: Strigiformes): dynamic repeat landscapes despite conserved karyotypes.

The elevated chromosome numbers observed in Tytonidae relative to the putative ancestral avian karyotype suggest that lineage-specific chromosomal fissions may have played an important role in the evolutionary history of this family. Here, we provide the first cytogenetic characterization of the American barn owl (Tyto furcata) and performs a comparative repeatome analysis across members of the Tytonidae, including other two species, the Western barn owl (Tyto alba), and the Oriental bay owl (Phodilus badius). The karyotype of T. furcata showed a 2n = 92, closely resembling that previously described for T. alba, indicating a high degree of chromosomal conservation within Tytonidae. Although T. furcata and T. alba exhibit similar karyotypic organization, comparative repeatomic analyses revealed differences in their composition, including variation in satellite DNA (satDNA) repertoires and abundance. Eight satDNA families were identified in T. furcata, nine in T. alba, and 28 in P. badius, highlighting the dynamic evolution of repetitive sequences. Several satDNA families were shared between T. furcata and T. alba, whereas some appeared species-specific, supporting the library hypothesis of satDNA evolution. In P. badius, multiple satDNAs exhibited similarity to transposable elements, suggesting that mobile elements contributed to their diversification. Cytogenetic analyses demonstrated centromeric heterochromatin distribution in T. furcata, as well as a large heterochromatic W chromosome enriched in DNA repeats. The localization of satDNAs in centromeric regions and the apparent accumulation of repeats on the W chromosome reinforce the role of repetitive sequences in chromosome organization and sex chromosome differentiation. Together, these findings reveal repeatome diversification despite conserved macrochromosomal structure and provide new insights into genome evolution and chromosomal dynamics in birds.

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PubMed2025

Expansion of satellite DNAs derived from transposable elements in beetles with reduced diploid numbers.

Repetitive DNA sequences are ubiquitous in eukaryotic genomes, significantly influencing their structure, function, and evolution. They can facilitate genomic rearrangements, contributing to chromosomal and genomic diversity. Chrysomelidae (Coleoptera) beetles are known for their highly diverse karyotypes and heterochromatin distribution. In this study, we advanced the understanding of the intricate relationship between satellite DNA-like sequences (named here solely as satDNA) and genome organization/reshuffling using three species of Eumolpinae chrysomelids. We investigated the satellitomes of three species with divergent karyotypes that had undergone independent chromosomal fusions: Colaspis laeta (2n = 22, Xyp), with a conserved karyotype; Endocephalus bigatus (2n = 10, neo-XY); and Iphimeis dives (2n = 14, neo-XY). Our comparative analysis revealed highly divergent patterns of satDNA origin, organization, and evolution. In species with reduced chromosome numbers and neo-sex chromosomes, we observed a high abundance of transposable element-related (TE-related) satDNAs. In Colaspis laeta, the sex chromosomes (Xyp) showed an advanced level of differentiation. However, in the species with a reduction in diploid number, such a level of differential enrichment of repetitive DNAs was not observed in the sex chromosomes, indicating an early stage of differentiation. Our findings support the hypothesis that chromosomal rearrangements and reorganization of repetitive DNA sequences are connected, with extensive reshuffling observed in species with reduced diploid numbers. Moreover, the data reinforce the involvement of TEs in satDNA origin, which could spread widely throughout the genome, including euchromatic areas. This study provides new insights into the evolutionary dynamics of repetitive DNAs in non-model species, emphasizing the impact of chromosomal rearrangements on genome architecture and evolution.

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PubMed2025

Repetitive DNAs and differentiation of the ZZ/ZW sex chromosome system in the combtail fish Belontia hasselti (Perciformes: Osphronemidae).

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.

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PubMed2026

Molecular divergence and genomic composition of B chromosomes in the fish Cyphocharax modestus (Characiformes, Curimatidae).

B chromosomes are supernumerary elements that evolve from standard A chromosomes and are primarily composed of repetitive DNAs, yet their origin, diversification, and molecular composition remain poorly understood in most vertebrates. We investigated two allopatric populations of Cyphocharax modestus (Curimatidae) combining classical cytogenetics, comparative genomic hybridization (CGH), and comparative satellitomics to characterize the repetitive DNA landscape of its B chromosomes. While both populations exhibited a conserved karyotype of 2n=54 biarmed chromosomes, five individuals from the Batalha River (BR) carried supernumerary chromosomes, comprising two distinct variants: a C-positive B1 and an C-negative B2. Comparative satellitome analysis between 3B-carrying and B-lacking individuals identified 116 satellite DNAs (CmoSatDNAs), with the 3B library showing higher abundances of specific sequences. Fluorescence in situ hybridization (FISH) revealed that both B variants share two centromeric satellites (CmoSat01-192 and CmoSat02-108) with the A complement, while CmoSat58-47 was exclusively to B2. Minimum spanning tree analysis of CmoSat58-47 revealed B-exclusive haplotypes alongside haplotypes shared with B-lacking individuals, suggesting a recent origin for these chromosomes. CGH experiments further confirm the sequence sharing between the A and B chromosomes, supporting an intraspecific origin, and revealing substantial genomic differentiation among B variants.

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