Search Results (58)

Satellite DNA is a dynamic component of plant genomes and a valuable source of cytogenetic markers, but its diversity and chromosomal distribution in polyploid Triticeae remain insufficiently studied. Here, low-coverage whole-genome sequencing, graph-based repeat clustering, quantitative PCR, multivariate statistics and fluorescence in situ hybridization (FISH) were used to identify and characterize satellite repeats in Elymus and related Triticeae species. Sixteen repeat clusters (E1–E16), with monomer lengths of 118–667 bp, showed distinct taxonomic distributions and copy-number profiles across 14 species. Correlation analysis, principal component analysis and hierarchical clustering revealed concerted variation among repeats and separated the perennial taxa Elymus and Pseudoroegneria from Triticum, Secale, Hordeum and Dasypyrum. Spearman correlation analysis identified E7 and E9 as putative candidates associated with St/StY genomic backgrounds, whereas E10 was identified as a putative candidate associated with the H genome. These statistical associations require independent cytogenetic validation. Contrasting copy numbers of E6 and E11 in bread wheat cv. Chinese Spring versus Dasypyrum villosum (L.) Candargy identified them as V-genome candidates. FISH localized E6 to the terminal regions of chromosomes 3VL, 4VS and 7VS, and E11 to 4VL. Karyotyping further revealed that two lines previously considered as wheat-D. villosum addition lines were in fact substitution lines: W3 was identified as a 3V(3D) substitution line and W4 as a 4V(4B) substitution line, whereas W7 retained its 7V addition status. These results expand the set of chromosomal markers for comparative genomics and introgression analysis in wheat. Full article

Skeletal muscle satellite cells (MuSCs) are essential for muscle growth and development, but their regulatory mechanisms remain unclear. This study aimed to characterize the expression pattern of pleomorphic adenoma gene 1 (PLAG1), determine its effects on MuSC proliferation and differentiation, and explore its potential regulatory mechanisms through integrated transcriptomic and ceRNA analyses in Sujiang pig MuSCs. Results showed that PLAG1 was widely expressed in multiple porcine tissues and was significantly upregulated during MuSC differentiation. PLAG1 overexpression promoted MuSC proliferation and differentiation, whereas PLAG1 knockdown produced the opposite effects. Whole-transcriptome sequencing following PLAG1 knockdown identified 432 differentially expressed mRNAs, 70 miRNAs, 163 lncRNAs, and 150 circRNAs. Enrichment analysis revealed that differentially expressed mRNAs were mainly associated with cell cycle regulation, DNA replication, and the p53 signaling pathway. Western blot analysis further showed that PLAG1 knockdown reduced CDK1 and PCNA protein levels. ceRNA network analysis revealed potential regulatory associations among differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs, and the expression changes in selected differentially expressed RNAs were further validated by qRT-PCR. Collectively, these findings indicate that PLAG1 promotes MuSC proliferation and differentiation and may be associated with cell cycle-related gene expression changes and potential non-coding RNA regulatory networks in porcine MuSCs. Full article

Satellite DNA (satDNA) is a family of tandemly repeated non-coding sequences in eukaryotic genomes involved in shaping genome architecture and regulation of various biological functions. Within a species, all satDNA families collectively form the satellitome. Satellitomes of Allium species has been explored only superficially, largely due to enormous genome sizes, high transposable element content, and a general lack of reference genomic resources. The emergence of reference genome assemblies now makes it possible to conduct a more in-depth study. Here, we applied a comprehensive bioinformatics approach to study the satellitomes of Allium cepa and Allium fistulosum. Using two complementary bioinformatics pipelines along with available reference genome assemblies, we have created the most complete collection of consensus satDNA sequences of A. cepa and A. fistulosum so far, consisting of 83 and 97 consensus sequences, respectively. The in silico analysis of the genomic distribution allowed the identification of 11 novel candidates for cytogenetic marker panels, including chromosome-specific satDNA families. Validation of satDNA using PCR and FISH confirmed the reliability of the created satellitomes. Furthermore, comparative analysis of satDNA genomic organization and abundance provided insights into the evolution of these species satellitomes. These findings provide a foundational resource that will help illuminate the evolutionary dynamics of Allium satellitomes and pave the way for future cytogenetic studies of Allium species. Full article

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. Full article

Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is an RNA-binding protein known to play critical roles in metabolism, cell proliferation, and tumorigenesis. Although its involvement in muscle development has been documented in several species, the function of goose IGF2BP2 remains largely unexplored. In this study, we cloned and characterized the full-length cDNA and genomic DNA sequences of goose IGF2BP2. The cDNA is 2957 bp in length and contains a 1662 bp open reading frame encoding a 553-amino acid protein with five conserved RNA-binding domains. The genomic sequence spans 12,183 bp and consists of 12 exons and 11 introns. A total of 60 genetic variants were identified, including a deletion of a G base at position 2299 (g.2299delG) that results in a frameshift mutation. Expression analysis revealed high levels of IGF2BP2 mRNA in the liver, heart, and muscle tissues of female geese across embryonic (E25d), growing (A70d), and laying (L270d) stages, consistent with a potential role in muscle development (p < 0.05). Functionally, overexpression of IGF2BP2 in skeletal muscle satellite cells (SMSCs) was associated with significant changes in the expression of several genes linked to muscle development and signaling pathways, including upregulation of IGF1, EGFR, FGF19, BMP6, BMP2, ACVR1C and WNT5A and downregulation of MYBPC3, NODAL, HOXD13, TNXB, and ADD2 (Padj < 0.01). Furthermore, protein–protein interaction (PPI) network analysis of these genes suggests that IGF2BP2 may coordinate key genes, contributing to its potential role in skeletal muscle development in geese. Full article

Background/Objectives: Satellite DNAs (satDNAs) are tandemly repeated sequences that play essential roles in chromosome structure, genome organization, and evolution. Despite their importance, the satellitome (the complete collection of satDNAs) of most avian lineages remains unexplored. We sought to describe the repeatome of three trogonid species, Trogon surrucura, T. melanurus, and Apaloderma vittatum with a focus on the satellitome to evaluate the general features of this lineage. Methods: Herein, we provide the first comparative characterization of the repeatome, with a particular focus on the comparative characterization of satDNAs in three trogonid species: T. surrucura, T. melanurus, and A. vittatum. Using a combination of bioinformatic pipelines and cytogenetic approaches. Results: We identified 16 satDNA families in T. surrucura, 15 in T. melanurus, and only 3 in A. vittatum. Sequence comparisons revealed that five families are shared between the two Trogon species, consistent with the library hypothesis, whereas no satDNAs were shared with A. vittatum. While both Trogon species exhibited a predominance of GC-rich repeats, A. vittatum represents the first bird described with a satellitome dominated by AT-rich satDNAs. In situ mapping in T. surrucura revealed chromosome-specific satDNAs restricted to pairs 1 and 2 and a Z-specific repeat that was strongly accumulated on its long arms, an atypical feature among birds. Conversely, the W chromosome showed a surprisingly low number of satDNAs, limited to centromeric signals. Conclusions: Our results reveal highly divergent satellitome landscapes among trogonids, characterized by lineage-specific differences in repeat composition, abundance, and chromosomal distribution. These findings support the view that satDNAs are dynamic genomic elements, whose amplification, loss, and chromosomal redistribution can influence genome architecture and play a role in avian speciation. Full article

Bats are great models for studying repetitive DNAs due to their compact genomes and extensive chromosomal rearrangements. Here, we investigated the repetitive DNA content of two phyllostomid bat species, Artibeus lituratus (2nn = 30♀/31♂) and Carollia perspicillata (2n = 20♀/21♂), both harboring a multiple XY₁Y₂ sex chromosome system. Satellite DNA (satDNA) libraries were isolated and characterized, revealing four and ten satDNA families in A. lituratus and C. perspicillata, respectively. These sequences, along with selected microsatellites, were in situ mapped onto chromosomes in both species and phylogenetically related taxa. SatDNAs showed strong accumulation in centromeric and subtelomeric regions, especially pericentromeric areas. Cross-species mapping with C. perspicillata-derived probes indicated terminal localization patterns in other bat species, suggesting conserved distribution. Microsatellites co-localized with 45S rDNA clusters on the neo-sex chromosomes. Additionally, genomic hybridization revealed a male-specific signal on the Y₁ chromosome, pointing to potential sex-linked repetitive regions. These findings confirm that bat genomes display relatively low amounts of repetitive DNA compared to other mammals and underscore the role of these elements in genome organization and sex chromosome evolution in phyllostomid bats. Full article

Background: Centromeric alpha satellite DNA is organized into higher-order repeats (HORs), whose precise structure is often difficult to resolve in standard genome assemblies. The recent telomere-to-telomere (T2T) assembly of the human genome enables complete analysis of centromeric regions, including the full structure of HOR arrays. Methods: We applied the novel high-precision GRMhor algorithm to the complete T2T-CHM13 assembly of human chromosome 21. GRMhor integrates global repeat map (GRM) and monomer distance (MD) diagrams to accurately identify, classify, and visualize HORs and their subfragments. Results: The analysis revealed a novel Cascading 11mer HOR array, in which each canonical HOR copy comprises 11 monomers belonging to 10 different monomer types. Subfragments with periodicities of 4, 7, 9, and 20 were identified within the array. A second, complex 23/25mer HOR array of mixed Willard’s/Cascading type was also detected. In contrast to the hg38 assembly, where a dominant 8mer and 33mer HOR were previously annotated, these structures were absent in the T2T-CHM13 assembly, highlighting the limitations of hg38. Notably, we discovered a novel 52mer HOR—the longest alpha satellite HOR unit reported in the human genome to date. Several subfragment repeats correspond to alphoid subfamilies previously identified using restriction enzyme digestion, but are here resolved with higher structural precision. Conclusions: Our findings demonstrate the power of GRMhor in resolving complex and previously undetected alpha satellite architectures, including the longest canonical HOR unit identified in the human genome. The precise delineation of superHORs, Cascading structures, and HOR subfragments provides unprecedented insight into the fine-scale organization of the centromeric region of chromosome 21. These results highlight both the inadequacy of earlier assemblies, such as hg38, and the critical importance of complete telomere-to-telomere assemblies for accurately characterizing centromeric DNA. Full article

Repetitive DNA represents over 50% of the human genome and is an abundant component of circulating cell-free DNA (cfDNA). We previously showed that cfDNA levels and integrity can predict survival in elderly patients with cardiovascular disease. Here, we aimed to clarify whether a low-pass next-generation sequencing (NGS) approach can characterize the repeat content of cfDNA. Considering the bimodal distribution of cfDNA fragment lengths, we examined the occurrence of repetitive DNA subfamilies separately in dinucleosomal (>250 bp) and mononucleosomal (≤250 bp) cfDNA sequences from 24 patients admitted for heart failure. An increase in the relative abundance of Alu repetitive elements was observed in the longer fraction, while alpha satellites were enriched in the mononucleosomal fraction. The relative abundance of Alu, ALR, and L1HS DNA in the dinucleosomal fraction correlated with different prognostic biomarkers, and Alu DNA was negatively associated with the presence of chronic kidney disease comorbidity. These results, together with the observed inverse correlation between Alu DNA abundance and cfDNA integrity, suggest that the composition of plasma cfDNA could be determined by multiple mechanisms in different physio-pathological conditions. In conclusion, low-pass NGS is an inexpensive method to analyze the cfDNA repeat landscape and identify new cardiovascular disease biomarkers. Full article

The genus Salvia L. (Lamiaceae) is characterized by complex taxonomy and controversial phylogeny. This genus includes about a thousand species with worldwide distribution and high ecological, structural, functional and morphological diversity. Because of their high content of essential oils, various Salvia plants are widely used in medicine, as well as in the food, perfume, cosmetic, and paint industries; they also are valuable melliferous resources. The present study reviews the taxonomic history of the genus Salvia and the phylogenetic relationships between the taxa within the subgenera Salvia, Sclarea, and Glutinaria. Among the Salvia species, three basic chromosome numbers, x = 7, x = 8, and x = 11, were most common, although other basic chromosome numbers (x = 6–19) were determined, which was probably due to events of dysploidy, aneupoidy, and/or polyploidy occurring during speciation. Recent molecular cytogenetic studies based on Next Generation Sequencing technologies have clarified the chromosomal organization of several Salvia species. The patterns of chromosome distribution of 45S rDNA, 5S rDNA, and satellite DNAs made it possible to assess their intra- and interspecific chromosome diversity. However, further cytogenetic studies are needed to characterize the chromosomes in the genomes of other Salvia species and specify the genomic relationships among them. Full article

The wolf fish Hoplias malabaricus is a Neotropical species characterized by remarkable karyotypic diversity, including seven karyomorphs (KarA-G) with distinct sex chromosome systems. This study investigated the homologous XY (KarF) and XY₁Y₂ (KarG) sex chromosome systems present in this species by integrating cytogenetics and genomics to examine sex chromosomes’ composition through characterization of repeatome (satellite DNA and transposable elements) and sex-linked markers. Our analysis indicated that both karyomorphs are little differentiated in their sex chromosomes content revealed by satDNA mapping and putative sex-linked markers. Both repeatomes were mostly composed of transposable elements, but neither intra- (male versus female) nor interspecific (KarF x KarG) variations were found. In both systems, we demonstrated the occurrence of sex-specific sequences probably located on the non-recombining region of the Y chromosome supported by the accumulation of sex-specific haplotypes of HmfSat10-28/HmgSat31-28. This investigation offered valuable insights by highlighting the composition of homologous XY and XY₁Y₂ multiple sex chromosomes. Although homologous, the large Y chromosome in KarF corresponds to two separate linkage groups (Y₁ and Y₂) in KarG implying a specific meiotic arrangement involving the X chromosome in a meiotic trivalent chain. This scenario likely influenced recombination rates and, as a result, the genomic composition of these chromosomes. Full article

Satellite DNAs (satDNAs) play a crucial role in understanding chromosomal evolution and the differentiation of sex chromosomes across diverse taxa, particularly when high karyotypic diversity occurs. The Physalaemus cuvieri–Physalaemus ephippifer species complex comprises at least seven divergent lineages, each exhibiting specific karyotypic signatures. The group composed of Ph. ephippifer, Lineage 1B of ‘Ph. cuvieri’ (L1B), and a lineage resulting from their secondary contact is especially intriguing due to varying degrees of sex chromosome heteromorphism. In this study, we characterized the satellitome of Ph. ephippifer in order to identify novel satDNAs that may provide insights into chromosomal evolution, particularly concerning sex chromosomes. We identified 62 satDNAs in Ph. ephippifer, collectively accounting for approximately 10% of the genome. Notably, nine satDNA families were shared with species from distantly related clades, raising questions about their potential roles in anurans genomes. Among the seven satDNAs mapped via fluorescent in situ hybridization, PepSat3 emerged as a strong candidate for the centromeric sequence in this group. Additionally, PepSat11 and PepSat24 provided evidence supporting a translocation involving both arms of the W chromosome in Ph. ephippifer. Furthermore, a syntenic block composed of PepSat3, PcP190, and PepSat11 suggested an inversion event during the divergence of Ph. ephippifer and L1B. The variation in signal patterns of satDNAs associated with nucleolar organizer regions (NORs) highlights the complexity of NOR evolution in this species complex, which exhibits substantial diversity in this genomic region. Additionally, our findings for PepSat30-350 emphasize the importance of validating the sex-biased abundance of satDNAs. Full article

Background: The order Suliformes exhibits significant karyotype diversity, with Sula species showing a Z₁Z₁Z₂Z₂/Z₁Z₂W multiple-sex chromosome system, an uncommon occurrence in avians. Satellite DNAs (satDNAs), which consist of tandemly repeated sequences, often vary considerably even among closely related species, making them valuable markers for studying karyotypic evolution, particularly that of sex chromosome evolution. This study aims to characterize and investigate the potential role of these sequences in the karyotypic evolution of the group, with special attention to the sex chromosomes. Methods: Through characterizing satDNAs in two Suliformes species (Sula leucogaster and Nannopterum brasilianum) using BGISEQ-500 platform and bioinformatics analysis. Their chromosomal distribution was mapped by fluorescence in situ hybridization (FISH) within their own karyotypes and in three additional Suliformes species (S. sula, S. dactylatra, and Fregata magnificens). Results: Five satDNAs were identified in S. leucogaster and eight in N. brasilianum. Within the genus Sula, three species shared specific satDNA sequences, although with different hybridization patterns. In contrast, the satDNAs of N. brasilianum were species-specific. Additionally, the Z chromosome, including Z₂ in Sula species, showed reduced accumulation of repetitive DNAs. Conclusions: These results suggest that differential accumulation of repetitive sequences may have contributed to the diversification of karyotypes in this group, particularly influencing the structure and differentiation of sex chromosomes. Full article

Chagas disease is a neglected disease caused by the parasite Trypanosoma cruzi, a public health problem in both endemic and non-endemic countries. In Mexico, the southern region is considered endemic, and cases are frequently reported; however, in the northwestern region, only a few cases are confirmed annually. This study describes, for the first time, the Discrete Typing Unit (DTU) of Trypanosoma cruzi in a volunteer blood donor rejected for being reactive in the northwestern region of Mexico. Seroreactivity was confirmed using “in-house” ELISAs which employed three different antigens: total extract from Trypanosoma cruzi isolated from a vector (Triatoma rubida) from Sonora (strain T1), strain H1 and CL-Brener. The molecular characterization of Trypanosoma cruzi was conducted by amplifying satellite DNA by qPCR and posterior sequencing of the mini-exon gene, using Next Generation Sequencing (NGS) to enhance the accuracy of genetic characterization. The results show that the reactive status of this blood donor was confirmed using our in-house ELISAs, and the presence of Trypanosoma cruzi by detecting TcI DTU confirmed the infection status. Full article

The ideal bacteriophages (phages) for the treatment of bacterial disease (phage therapy) would bypass bacterial evolution to phage resistance. However, this feature (called a hyper-aggression feature) has never been observed to our knowledge. Here, we microbiologically characterize, fractionate, genomically classify, and perform electron microscopy of the newly isolated Bacillus thuringiensis phage 0524phi7-1, which we find to have this hyper-aggression feature. Even visible bacterial colonies are cleared. Phage 0524phi7-1 also has three other features classified under hyper-aggression (four-feature-hyper-aggressive phage). (1) Phage 0524phi7-1 forms plaques that, although sometimes beginning as semi-turbid, eventually clear. (2) Clear plaques continue to enlarge for days. No phage-resistant bacteria are detected in cleared zones. (3) Plaques sometimes have smaller satellite plaques, even in gels so concentrated that the implied satellite-generating phage motion is not bacterial host generated. In addition, electron microscopy reveals that phage 0524phi7-1 (1) is a myophage with an isometric, 91 nm-head (diameter) and 210 nm-long contractile tail, and (2) undergoes extensive aggregation, which inhibits typical studies of phage physiology. The genome is linear double-stranded DNA, which, by sequencing, is 157.103 Kb long: family, Herelleviridae; genus, tsarbombavirus. The data suggest the hypothesis that phage 0524phi7-1 undergoes both swimming and hibernation. Techniques are implied for isolating better phages for phage therapy. Full article