Search Results (129)

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

Investigations of endogenous plant circular RNAs (circRNAs) in several plant species have revealed changes in their circular RNA profiles in response to biotic and abiotic stresses. Recently, circRNAs have emerged as critical regulators of gene expression. The destructive impacts on agriculture due to plant viral infections necessitate better discernment of the involvement of plant circRNAs during viral infection. However, few such studies have been conducted hitherto. Sobemoviruses cause great economic impacts on important crops such as rice, turnip, alfalfa, and wheat. Our current study investigates the dynamics of plant circRNA profiles in the host Arabidopsis thaliana (A. thaliana) during infections with the sobemoviruses Turnip rosette virus (TRoV) and Rice yellow mottle virus (RYMV), as well as the small circular satellite RNA of the Lucerne transient streak virus (scLTSV), focusing on circRNA dysregulation in the host plants and its potential implications in triggering plant cellular defense responses. Towards this, two rounds of deep sequencing were conducted on the RNA samples obtained from infected and uninfected plants followed by the analysis of circular RNA profiles using RNA-seq and extensive bioinformatic analyses. We identified 760 circRNAs, predominantly encoded in exonic regions and enriched in the chloroplast chromosome, suggesting them as key sites for circRNA generation during viral stress. Gene ontology (GO) analysis indicated that these circRNAs are mostly associated with plant development and protein binding, potentially influencing the expression of their host genes. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed photosynthesis as the most affected pathway. Interestingly, the non-coding exogenous scLTSV specifically induced several circRNAs, some of which contain open reading frames (ORFs) capable of encoding proteins. Our biochemical assays demonstrated that transgenic expression of scLTSV in A. thaliana enhanced resistance to TRoV, suggesting a novel strategy for improving plant viral resistance. Our results highlight the complexity of circRNA dynamics in plant–virus interactions and offer novel insights into potential circRNA-based strategies for enhancing plant disease resistance by modulating the differential expression of circRNAs. 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

Tandemly repeated DNA fragments are major components of centromeres and pericentromeric heterochromatin, which is responsible for chromosomal stability and segregation. Recent evidence suggests that transcripts from these repeats play a key role in heterochromatin maintenance, and these repeats can be highly dynamic with various copy numbers. Here, we developed a mathematical model for human satellite repeats, which tracks the silenced and desilenced repeats, lncRNA, and copy number. Our model shows that chromatin factors for silencing and RNA stability can facilitate copy gain in satellites. Also, the system can be bistable, and cells with different copy numbers, silenced repeats with a small copy number, and desilenced repeats with a large copy number may coexist. To incorporate the cooperative methylation by neighboring repeats and the local chromatin environment, we also developed a spatial model where the local chromatin environment facilitates methylation locally. This model suggests that a local domain of silenced repeats may be an important feature of copy number regulation. Our models suggest that pericentromeric repeats are highly dynamic, and small changes in chromatin regulation can lead to large changes in satellite copy numbers. Full article

Active space debris removal is now integral to modern space exploration. In order to address the problem of a heterogeneous satellite swarm with different payloads carrying out the emergency active removal of space debris, this paper proposes a Multi-type Chromosome Fast Elitist Non-Dominated Sorting Genetic Algorithm (MC-NSGA-II). The algorithm is designed to enable the satellite swarm to execute multiple coupled tasks in succession with improved optimization efficiency. An arbitrary execution order may result in deadlock, where one or more satellites become trapped in an infinite waiting loop. In order to address the heterogeneous problem of satellites and task coupling constraints, a multi-type chromosome coding strategy is developed. To evaluate different allocation strategies, three optimization objectives—time consumption, fuel consumption, and task balance—are introduced. To align with the multi-type chromosome coding strategy, two distinct sorting methods are developed for crossover and mutation operations, ensuring that all offspring individuals meet the constraints. Additionally, the algorithm incorporates a dynamic parameter-setting strategy to enhance solution efficiency. Finally, comparative simulations validate the effectiveness and superiority of the proposed method. The results show that the high-quality solution search ability of the MC-NSGA-II algorithm is 23.07% higher than that of the standard NSGA-II algorithm. Full article

Background/Objectives: Paspalum notatum is a key multipurpose species native to American grasslands. This study provides, for the first time, a detailed karyotype analysis of diploid (2n = 2x = 20) and tetraploid (2n = 4x = 40) accessions of P. notatum, the most common cytotypes within the species. Methods: The constitutive heterochromatin patterns revealed using CMA-DA-DAPI staining and genome size estimations are novel contributions to the understanding of the N genome in Paspalum. Results: Chromosomes were small (1.1–2.3 µm), with the diploid karyotype comprising nine metacentric pairs (one bearing microsatellites on the short arms, pair 6) and one submetacentric pair. In tetraploids, the diploid karyotype was duplicated. Heterochromatin analysis revealed two CMA⁺⁺/DAPI⁻ bands located on the short arm and satellite of chromosome 6 in diploids, while tetraploids exhibited two to three CMA⁺⁺/DAPI⁻ and one to two CMA⁺⁺/DAPI⁰ bands. The proportion of GC-rich heterochromatin represented 2.8 and 3.47% of the total chromosome length in diploid and tetraploid cytotypes, respectively. Genome size analysis revealed a reduction in monoploid genome size in tetraploids (1Cx = 0.678 pg) compared to diploids (1Cx = 0.71 pg), consistent with the autopolyploid origin hypothesis. Conclusions: These findings provide essential cytogenetic insights and suggest only minor structural changes in the N genome following polyploidization, which could guide future studies integrating genomic and cytogenetic maps of P. notatum. Full article

Background/Objectives: A striking feature of the karyotypes of stingless bees is the large amount of heterochromatin present in most species. Cytogenomic studies performed in some Meliponini species have suggested that evolutionary events related to the diversification and amplification of satellite DNA families in the heterochromatin may reflect the structuring of phylogenetic clades in this tribe. In this study, we performed a genomic analysis in Frieseomelitta varia to characterize different satDNA families in its genome. We also investigated the presence of the most abundant satDNA family of F. varia in its own chromosomes, in two other Frieseomelitta species, and in other Meliponini genera encompassing the three main clades of Neotropical Meliponini, according to the available molecular phylogeny. Methods: Genomic analyses were performed using RepeatExplorer2 on the Galaxy platform, and chromosomal investigations were conducted using fluorescent in situ hybridization. Results: Seven satDNA families were recovered, which together totaled an abundance of 11.223% of the analyzed F. varia genomic fraction. The most abundant satDNA family, FvarSat01-306, predominates in the analyzed repetitive fraction (representing around 89%) and was recently amplified and homogenized in almost all the heterochromatin of F. varia. In addition, the data revealed an unprecedented sharing of this satDNA family in the centromeric/pericentromeric heterochromatin among different Meliponini genera, with independent amplifications and loss of this sequence in some taxa. Conclusions: One family of satellite DNA makes up most of the heterochromatin in this species and is shared with other Meliponini. Full article

Amaranthus cruentus L. and Amaranthus hypochondriacus L. are valuable and promising food crops for multi-purpose use that are distributed worldwide in temperate, subtropical, and tropical zones. However, their karyotypes and genomic relationships still remain insufficiently studied. For the first time, a comparative repeatome analysis of A. cruentus and A. hypochondriacus was performed based on the available NGS data; bioinformatic analyses using RepeatExplorer/TAREAN pipelines; and chromosome FISH mapping of 45S rDNA, 5S rDNA, and the most abundant satellite DNAs. In the repeatomes of these species, interspecific variations in the amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were detected. In the repeatomes of both species, shared satDNAs with high sequence similarity were identified. The chromosome distribution patterns of four effective molecular markers, 45S rDNA, 5S rDNA, AmC4, and AmC9, allowed us to identify all chromosome pairs in the species karyotypes, construct unique karyograms of A. cruentus and A. hypochondriacus, and confirm the close relationship between their genomes. These results are important for comparative karyotypic studies within the genus Amaranthus. Our findings demonstrated that cytogenomic analyses might provide important data on genomic relationships within Amaranthus and increase knowledge on genome organization in these valuable crops. Full article

The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) are responsible for the development of skeletal muscle. In our previous study, circ_002156 was found to be highly expressed in caprine Longissimus Dorsi muscle, but the regulatory role of the circular RNAs (circRNA) in goat SMSCs remains unclear. In this study, the authenticity of circ_002156 was validated, and its structurally characteristic and cellular localization as well as tissue expression of circ_002156 and its parent genes were investigated. Moreover, the effects of circ_002156 on the viability, proliferation, and differentiation of SMSCs were also studied. The circ_002156 is located on caprine chromosome 19 with a length of 36,478. The circRNA structurally originates from myosin heavy chain 2 (MYH2), MYH1, and MYH4 as well as intergenic sequences among the parent genes. RT-PCR and Sanger sequencing confirmed the authenticity of circ_002156. Most circ_002156 (55.5%) was expressed in the nuclei of SMSCs, while 44.5% of circ_002156 was located in the cytoplasm. The circ_002156 and its three parent genes had higher expression levels in the triceps brachii, quadriceps femoris, and longissimus dorsi muscle tissues than in the other five tissues. The expression of circ_002156 and its parent genes MYH1 and MYH4 reached the maximum on day 8 of differentiation, while MYH2 in expression reached the peak on day 4 after differentiation. The Pearson correlation coefficients revealed that circ_002156 had moderate or high positive correlations with the three parent genes in the expression of both quadriceps femoris muscle and SMSCs during different differentiation stages. The small interfering RNA circ_002156 (named si-circ_002156) remarkably increased the viability of the SMSCs. The si-circ_002156 also increased the number and parentage of Edu-labeled positive SMSCs as well as the expression levels of four cell proliferation marker genes. These suggest that circ_002156 inhibited the proliferation of SMSCs. Meanwhile, si-circ_002156 decreased the area of MyHC-labeled positive myotubes, the myotube fusion index, and myotube size as well as the expression of its three parent genes and four cell differentiation marker genes, suggesting a positive effect of circ_002156 on the differentiation of SMSCs. This study contributes to a better understanding of the roles of circ_002156 in the proliferation and differentiation of SMSCs. Full article

The cosmopolitan genus Hedysarum L. (Fabaceae) is divided into sections Hedysarum, Stracheya, and Multicaulia. This genus includes many valuable medicinal, melliferous, and forage species. The species taxonomy and genome relationships within the sections are still unclear. We examined intra- and interspecific diversity in the section (sect.) Hedysarum based on repeatome analyses using NGS data, bioinformatic technologies, and chromosome FISH mapping of 35S rDNA, 5S rDNA, and the identified satellite DNA families (satDNAs). A comparison of repeatomes of H. alpinum, H. theinum, and H. flavescens revealed differences in their composition. However, similarity in sequences of most satDNAs indicated a close relationship between genomes within sect. Hedysarum. New effective satDNA chromosomal markers were detected, which is important for karyotype analyses within Hedysarum. Intra- and interspecific variability in the chromosomal distribution patterns of the studied markers were revealed, and species karyograms were constructed. These results provided new insight into the karyotype structures and genomic diversity within sect. Hedysarum, clarified the systematic position of H. sachalinense and H. arcticum, and confirmed the distant genomic relationships between species from sections Hedysarum and Multicaulia. Our findings are important for further comparative genome studies within the genus Hedysarum. Full article

Background: The Neuro-2a cell line, derived from a murine neuroblastoma (NB), was established as early as 1969 and originates from a transplantable tumor that arose spontaneously in an A/Jax male mouse in 1940. Since then, it has been applied in over 10,000 studies and is used by the World Organization for Animal Health for the routine diagnosis of rabies. Surprisingly, however, Neuro-2a has never been genetically characterized in detail; this study fills that gap. Methods: The Neuro-2a cell line and two of its derivatives, Neuro-2a TR-alpha and Neuro-2a TR-beta, were analyzed for their chromosomal constitution using molecular cytogenetic approaches. Array comparative genomic hybridization was performed to characterize copy number alterations. Results: Neuro-2A has a hyper-tetraploid karyotype with 70 to 97 chromosomes per cell, and the karyotypes of its two examined derivatives were quite similar. Neither of them had a Y-chromosome. The complex karyotype of Neuro-2a includes mitotically stable dicentres, neocentrics, and complex rearrangements resembling chromothripsis events. Although no amplification of euchromatin or oncogenes was detected, there are five derivative chromosomes with the amplification of centromere-near heterochromatic material and 1–5 additional derivatives consisting only of such material. Conclusions: Since satellite DNA amplification has recently been found in advanced human tumors, this finding may be the corresponding equivalent in mice. An in silico translation of the obtained results into the human genome indicated that Neuro-2A is suitable as a model for advanced human NB. Full article

A new hexaploid cytotype of Aegilops crassa has been identified in Türkiye. To assess the ploidy levels of native populations, 50 samples from Adıyaman, Batman, Bitlis, Diyarbakır, Hakkari, Mardin, Siirt, Şanlıurfa, Şırnak, and Van were analyzed using flow cytometry and cytogenetic techniques. DNA content was determined by comparison with standard plants. Results confirmed two cytotypes in Türkiye: tetraploid populations from Batman, Bitlis, Diyarbakır, Hakkari, Mardin, Siirt, Şanlıurfa, and Şırnak, and hexaploid accessions from Adıyaman and Van. Ten metaphase plates were analyzed. The tetraploid cytotype exhibited chromosome lengths of 8.95 ± 0.27 to 13.96 ± 0.13 µm, a total genome length of 165.51 ± 0.34 µm, and nuclear DNA content of 18.53 ± 0.29 to 20.37 ± 0.49 pg. Most chromosomes were metacentric, except for chromosomes 7, 8, 10, and 12, which were submetacentric. Two satellite pairs were found on chromosomes 4 and 10. The hexaploid cytotype showed chromosome lengths of 8.90 ± 0.16 to 14.06 ± 0.06 µm, a total genome length of 230.47 ± 0.23 µm, and nuclear DNA content of 33.40 ± 0.52 to 35.01 ± 0.31 pg. Most chromosomes were also metacentric, with three satellite pairs on chromosomes 3, 6, and 10. In conclusion, both tetraploid (2n = 2x = 28) and hexaploid (2n = 6x = 42) cytotypes of Ae. crassa exist in Türkiye, with the hexaploid cytotype having potential for wheat breeding programs. Full article