Pablo Mora

Background/Objectives: Flea beetles (Coleoptera, Chrysomelidae: Alticinae) show extensive karyotypic diversity, yet cytogenetic and genomic data remain scarce for many taxa. Species of the genus Podagrica are characterized by unusually high chromosome numbers compared with the modal condition in Alticinae, suggesting a history of chromosomal fissions. This study aimed to characterize the karyotype and repetitive DNA composition of Podagrica fuscicornis, with special emphasis on the satellitome and its contribution to chromosome organization. Methods: Male specimens of P. fuscicornis collected in southern Spain were analyzed using conventional cytogenetic techniques, including Giemsa staining, DAPI staining, and C-banding. Fluorescence in situ hybridization was employed to map nucleolar organizer regions (NORs), telomeric repeats, and major satellite DNA (satDNA) families. The satellitome was characterized using Illumina short-read sequencing and analyzed with the RepeatExplorer2/TAREAN pipeline to identify satDNA families and estimate their genomic abundance and divergence. Results: The male karyotype of P. fuscicornis was 2n = 40 (38 + XY), with an Xy_p sex chromosome system. Constitutive heterochromatin was mainly pericentromeric, and the Y chromosome was largely heterochromatic. NORs were located on a single autosomal pair, and the ancestral insect telomeric motif (TTAGG)_n was detected at chromosome ends. The satellitome comprised at least 70 different satDNA families, representing 9.51% of the genome, some of them related to transposable elements. Ten of these 70 satDNAs are shared in other Alticinae species. The most abundant families were primarily localized in pericentromeric regions and showed differential distribution between autosomes and sex chromosomes. Conclusions: These results indicate that extensive chromosomal fissions and high satDNA dynamics could drive the high chromosome number and heterogeneous genome organization in P. fuscicornis, highlighting the role of repetitive DNA in karyotype evolution within Chrysomelidae.

This study reports for the first time the complete sequencing of the mitogenome of three Oestridae species: Cephenemyia auribarbis , C. ulrichii , and Pharyngomyia picta (Diptera: Oestridae). These three mitogenomes were assembled and annotated from specimens collected in southern and northern Spain ( C. auribarbis and P. picta , respectively) and in Russia ( C. ulrichii ). They were then compared with the mitogenomes of 18 other Oestridae species available in GenBank. All three analyzed mitogenomes exhibited a conserved gene content and structure comprising 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region, with a high A + T content characteristic of the Oestridae. Intraspecific variability in length and sequence was detected in C. ulrichii and P. picta . Comparative analyses revealed conserved start/stop codons and consistent PCGs, tRNA, and rRNA gene organization. The D-loop region had the highest sequence variability. The phylogenetic analyses of 24 complete mitogenomes confirmed the monophyly of the genus Cephenemyia , with Pharyngomyia as its closest relative. Together, these genera formed a well-supported clade with Oestrus and Rhinoestrus . These results served to reinforce previously postulated phylogenetic hypotheses and underscored the utility of mitogenomic data in resolving the evolutionary relationships within the Oestridae. The mitogenomes described in this study offer significant molecular resources for future research into the taxonomy, phylogeny, and molecular evolution of bot flies.

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, Xy_p), 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 (Xy_p) 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.

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.

Satellite DNAs (satDNAs), ubiquitous sequences in eukaryotic genomes, play a crucial role in genome organization, function, and evolution. The pea aphid Acyrthosiphon pisum is a major crop pest, and an emerging model for ecological, developmental, and evolutionary studies. This study characterizes the satellitome of the A. pisum to better understand its genomic organization and the evolutionary dynamics of satDNAs at the intraspecies level. The analysis of satDNAs across various host-plant adapted biotypes reveals a general sharing of the satellitome, with significative quantitative differences. We observe the amplification or contraction of specific satDNA families, even in the same biotype, consistent with the fast-evolutionary changes characteristic of these sequences. Rapid differential accumulation of repetitive elements among biotypes together with other factors may contribute to the origin of genetic incompatibilities. At the interspecific level, fluctuations in satDNA abundances, including the loss of certain families, are consistent with the library hypothesis, long-term conservation, and differential amplification of an ancestral satellitome. SatDNAs are considerably enriched in the heterochromatin of the chromosome X (Chr-X) and to a less extent, dispersed across the euchromatic region of all chromosomes. The enrichment of these sequences on Chr-X also features the elements that are most recently amplified and homogenized. This suggests that Chr-X could serve as a fountain of youth for satDNAs, contributing to the “fast-X” effect. Our findings provide valuable insights into genome structure, assembly, and the potential impact of satDNAs on species diversification, as well as the evolution of autosomes and Chr-X.

The genome of Triatoma rubrofasciata , a representative of the North American Triatomini lineage, was analysed to characterise its repetitive DNA content and satellite DNA (satDNA) organisation. Using RepeatExplorer2, we determined that repetitive elements comprise approximately 25% of the genome in a male sample from Vietnam and 16% in a female sample from China, with satDNA being the most abundant component. The satellitome analysis revealed 126 satDNA families in the male and 114 in the female, with marked quantitative differences driven by the amplification of two satDNA families: TrubSat001‐166 and TrubSat002‐9. Fluorescence in situ hybridization (FISH) confirmed that TrubSat002‐9 is enriched in the Y chromosome, explaining its lesser abundance in the female genome. Chromosomal mapping revealed three distribution patterns of satDNA: (i) localisation in autosomal heterochromatin, (ii) restriction to the Y chromosome, and (iii) presence in euchromatin. SatDNA landscapes showed sharp peaks at low divergence values, consistent with recent amplifications in heterochromatic regions, and broader peaks at higher divergence levels, suggesting older satDNAs located in euchromatic regions. Additionally, several satDNA families are conserved among T. rubrofasciata , T. infestans , T. delpontei and Rhodnius prolixus , supporting the “library hypothesis” of satDNA evolution. Our findings highlight the differential amplification of satDNA families linked to heterochromatin expansion, particularly in autosomes, and the conservation of Y‐linked repeats. This study provides new insights into the dynamic role of satDNAs in the karyotypic evolution of Triatominae bugs.

Sphaerophoria rueppellii is a Palearctic hoverfly widely used as a native biocontrol agent against aphid pests in Mediterranean agroecosystems. In this study, we present a cytogenetic analysis and characterization of the mitochondrial genome of this species. Chromosomal preparations, obtained from third-instar larvae, were used for conventional staining, DAPI staining and C-banding techniques, and major ribosomal DNA (rDNA) location by fluorescence in situ hybridization (FISH). Karyotype analysis revealed a diploid number of 2n = 10, with heterochromatic blocks in the pericentromeric regions of all autosomes and rDNA clusters on both sex chromosomes. The complete mitochondrial genome (16,605 bp) was sequenced and annotated using next-generation sequencing and assembly pipelines. It contains the typical 37 mitochondrial genes and a highly A + T-rich control region with tandem repeats. Gene order and codon usage were conserved compared with other Syrphidae. Phylogenetic reconstruction based on mitochondrial protein-coding genes clarifies the species’ placement within the Syrphini tribe. Our results contribute valuable genomic and cytogenetic information that supports comparative analyses and may aid in taxonomic clarification within the genus. These findings also offer key data that could guide the genetic optimization of S. rueppellii as an efficient, environmentally safe biological control agent in sustainable agriculture.

Despite the economic and scientific importance of Bombyx mori , its satellite DNA (satDNA) fraction remains poorly characterized. Here, we present the first comprehensive analysis of the B. mori satellitome, revealing its low abundance (∼0.76%), A+T enrichment, high monomer size variability, and predominantly dispersed chromosomal organization. Comparative analysis with B. mandarina , the wild ancestor of B. mori , demonstrated high satDNA conservation in abundance and sequence composition, despite speciation and domestication events. Divergence landscapes of satDNA sequences indicate predominantly ancient amplifications with few recent homogenization events. SatDNA families exhibited low strain differentiation across five B. mori strains, exemplified by the consistent presence and abundance of BmorSat01-575 and BmorSat29-84. The W chromosome was identified as a hotspot for satDNA accumulation, especially BmorSat24-753, which showed female-specific amplification and higher sequence homogeneity, suggesting functional or structural roles in W chromosome evolution. In contrast, the Z chromosome displayed similar satDNA content to autosomes, with two families being exclusive to this chromosome and conserved in both Bombyx species. Remarkably, some of B. mori satDNAs were found to be derived from transposable elements (TEs), supporting the hypothesis of TE-driven satDNA origin via multiple mechanisms, including tandemization of TE fragments. Our findings underscore the dynamic interplay between satDNAs and TEs in shaping genome architecture, the stability of the satellitome through domestication, and the sex chromosome-specific accumulation patterns. These insights lay the groundwork for future studies investigating the functional roles of satDNAs in genome regulation and chromatin dynamics in Lepidoptera.