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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 October 2025) | Viewed by 8231

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Special Issue Editors

Dr. Eva Šatović-Vukšić

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Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: repetitive DNA sequences; satellite DNA; transposable elements; heterochromatin; NGS; satellitome; repeatome; genome biology; genome evolution, bivalves, insects
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Prof. Dr. Miroslav Plohl

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Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: repetitive DNA sequences; satellite DNAs; mobile elements; heterochromatin; centromere; telomere; satellitome; evolution of repetitive sequences
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Prof. Dr. Manuel A. Garrido-Ramos

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Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
Interests: satellite DNA; repetitive DNA sequences; genome evolution; centromeres; telomeres; plastomes; mitogenomes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Repetitive DNA sequences, a major component of eukaryotic genomes, play important roles in genome structure, function, and evolution. These sequences, including satellite DNAs, transposable elements, and multigene families, contribute to genome complexity in many ways. Repetitive DNA sequences influence chromosomal architecture, participate in genome rearrangements, modulate gene expression, and serve as constitutive components of centromeres, telomeres, heterochromatin, as well as euchromatin. The dynamic nature of repetitive DNA sequences makes them vital to understanding evolutionary processes. Advances in genome sequencing and bioinformatics approaches, in combination with chromatin immunoprecipitation, RNA-seq, cytogenetic and phylogenetic studies, further our ability to analyze repetitive regions, revealing their evolutionary history, organization, functions, and structural roles. By integrating diverse approaches and different omics studies, researchers continue to uncover the diverse contributions and significance of repetitive DNA sequences. This Special Issue invites submissions of articles on different topics that advance our knowledge on repetitive DNA sequences and their influence on genome biology and evolution.

Dr. Eva Šatović-Vukšić
Prof. Dr. Miroslav Plohl
Prof. Dr. Manuel A. Garrido-Ramos
Guest Editors

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Keywords

repetitive DNA sequences
satellite DNA
transposable elements
heterochromatin
centromere
satellitome
repeatome
cytogenetics
phylogenetics
transcription
ChIP
bioinformatics
genome biology
genome evolution

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Published Papers (8 papers)

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Research

Jump to: Review

13 pages, 1246 KB

Open AccessArticle

Downregulation of Gene Expression by Alpha Satellite Transcripts

by Sven Ljubić, Maja Matulić, Damir Đermić, Maria Chiara Feliciello, Alfredo Procino, Francesco Passaro, Đurđica Ugarković and Isidoro Feliciello

Int. J. Mol. Sci. 2025, 26(22), 11204; https://doi.org/10.3390/ijms262211204 - 20 Nov 2025

Viewed by 298

Abstract

Satellite DNAs are highly abundant sequences that build functional centromeres and pericentromeric heterochromatin in many eukaryotes. Apart from this structural role, their involvement in gene expression modulation has been demonstrated, although a detailed understanding of the molecular mechanisms is still lacking. Here, using the major human alpha satellite as a model system, we investigate the role of satellite transcripts in gene expression regulation. We generated cell lines with forced, exogenous overexpression of alpha satellite RNA and followed the expression levels of genes containing alpha satellite repeats within introns. Our results reveal a positive correlation between exogenous alpha satellite expression and the downregulation of alpha-associated genes, strongly suggesting that alpha satellite RNA affects their transcription. Notably, the elevated levels of exogenous alpha satellite RNA did not affect histone modifications characteristic of pericentromeric heterochromatin (e.g., H3K9me3 or H3K18Ac) or euchromatin (e.g., H3K4me2) at intronic alpha satellite loci. We propose that alpha satellite RNA directly interacts with homologous DNA at dispersed intronic satellite loci by forming RNA-DNA hybrid structures, which may affect chromatin structure and transcriptional activity. The results demonstrate that alpha satellite RNA is not only involved in centromere and heterochromatin assembly but, as shown here for the first time, also plays a role in modulating the expression of alpha-associated genes. Full article

(This article belongs to the Special Issue Repetitive DNA)

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19 pages, 4292 KB

Open AccessArticle

Comparative Analysis of Chromosome Repeat DNA Patterns in Four Amaranthus Species

by Alexandra V. Amosova, Olga Yu. Yurkevich, Alexey R. Semenov, Murat S. Gins, Julia V. Kalnyuk, Lyudmila V. Zemtsova, Alexander I. Morozov, Ekaterina D. Badaeva, Svyatoslav A. Zoshchuk and Olga V. Muravenko

Int. J. Mol. Sci. 2025, 26(22), 11026; https://doi.org/10.3390/ijms262211026 - 14 Nov 2025

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Abstract

Amaranthus L. includes valuable and promising crops of multi-purpose use, having high morphological diversity and complicated taxonomy. Their karyotypes and genomic relationships remain insufficiently studied. For the first time, a comparative repeatome analysis of Amaranthus tricolor L., Amaranthus cruentus L., and Amaranthus hypochondriacus L. was performed based on the high-throughput sequencing data obtained via bioinformatic analyses using the RepeatExplorer2/TAREAN/DANTE_LTR pipelines. Interspecific variations in the abundance of Ty1 Copia and Ty3 Gypsy retroelements, DNA transposons, and ribosomal and satellite DNA (satDNA) were detected. Based on fluorescence in situ hybridization (FISH), chromosome mapping of 45S rDNA, 5S rDNA, and satDNAs AmC9 and AmC70, and unique karyograms of A. tricolor, A. cruentus, Amaranthus paniculatus L., and A. hypochondriacus were constructed. The analysis of the interspecies genome diversity/similarity in DNA repeat contents, sequences of the identified satDNAs, and chromosome distribution patterns of the studied molecular markers indicated that these species might also share a common evolutionary ancestor. However, the genomes of A. cruentus, A. paniculatus, and A. hypochondriacus were more similar compared to A. tricolor, which aligns with the previous phylogenetic data. Our results demonstrate that cytogenomic studies might provide important data on Amaranthus species relationships elucidating taxonomy and evolution of these valuable crops. Full article

(This article belongs to the Special Issue Repetitive DNA)

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16 pages, 3294 KB

Open AccessArticle

Integration of Repeatome and Cytogenetic Data on Tandem DNAs in a Medicinal Plant Polemonium caeruleum L.

by Olga V. Muravenko, Alexandra V. Amosova, Alexey R. Semenov, Julia V. Kalnyuk, Firdaus M. Khazieva, Irina N. Korotkikh, Irina V. Basalaeva, Ekaterina D. Badaeva, Svyatoslav A. Zoshchuk and Olga Yu. Yurkevich

Int. J. Mol. Sci. 2025, 26(18), 9240; https://doi.org/10.3390/ijms26189240 - 22 Sep 2025

Viewed by 599

Abstract

Polemonium caeruleum L. (Polemoniaceae) is a perennial flowering plant native to Eurasia and North America, which is used as a fodder, medicinal, and ornamental plant. Many issues related to the taxonomy and origin of this valuable species still remain unclear. The intraspecific genetic variability of P. caeruleum and chromosomal organization of its genome are insufficiently studied. For the first time, we analyzed NGS genomic data of P. caeruleum using ReapeatExplorer2/TAREAN/DANTE Pipelines. In its repeatome, we identified 66.08% of Class I retrotransposons; 0.57% of Class II transposons; 0.42% of ribosomal DNA; and 0.87% of satellite DNA (six high-confident and three low-confident putative satellite DNAs). FISH chromosome mapping of seven tandem DNAs was carried out in two P. caeruleum varieties and two wild populations. Our results demonstrated the effectiveness of using satDNAs Pol_C 46 and Pol_C 33 in combination with 45S rDNA and 5S rDNA for precise chromosome identification. This approach allowed us to study intraspecific chromosomal variability and detect chromosomal rearrangements in the studied accessions of P. caeruleum, which could be related to the speciation process. These novel molecular markers are important for chromosome studies within Polemonium to clarify its taxonomy and phylogeny, and also, they expand the potential of different breeding programs. Full article

(This article belongs to the Special Issue Repetitive DNA)

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18 pages, 2910 KB

Open AccessArticle

Repeatome Dynamics and Sex Chromosome Differentiation in the XY and XY₁Y₂ Systems of the Fish Hoplias malabaricus (Teleostei; Characiformes)

by Mariannah Pravatti Barcellos de Oliveira, Geize Aparecida Deon, Francisco de Menezes Cavalcante Sassi, Fernando Henrique Santos de Souza, Caio Augusto Gomes Goes, Ricardo Utsunomia, Fábio Porto-Foresti, Jhon Alex Dziechciarz Vidal, Amanda Bueno da Silva, Tariq Ezaz, Thomas Liehr and Marcelo de Bello Cioffi

Int. J. Mol. Sci. 2025, 26(13), 6039; https://doi.org/10.3390/ijms26136039 - 24 Jun 2025

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Abstract

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

(This article belongs to the Special Issue Repetitive DNA)

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25 pages, 9238 KB

Open AccessArticle

DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst in Arabidopsis thaliana

by Pavel Merkulov, Anastasiia Latypova, Kirill Tiurin, Melania Serganova and Ilya Kirov

Int. J. Mol. Sci. 2025, 26(10), 4816; https://doi.org/10.3390/ijms26104816 - 17 May 2025

Cited by 2 | Viewed by 2365

Abstract

Transposable elements (TEs) are major drivers of plant genome plasticity, but the immediate molecular consequences of new TE insertions remain poorly understood. In this study, we generated a wild-type Arabidopsis thaliana population with novel insertions of ONSEN retrotransposon to investigate early epigenomic and transcriptomic changes using whole-genome and cDNA nanopore sequencing. We found that novel ONSEN insertions were distributed non-randomly, with a strong preference for genic regions, particularly in chromatin enriched for H2A.Z, H3K27me3, and H3K4me2. Most full-length ONSEN insertions within genes were rapidly recognized and spliced out as new introns (intronization), thereby mitigating potential deleterious effects on transcript isoforms. In some cases, ONSEN insertions provided alternative transcription start or termination sites, generating novel transcript isoforms. Genome-wide methylation analysis revealed that new ONSEN copies were efficiently and precisely targeted by DNA methylation. Independently on the location of the original ONSEN element, the euchromatic and heterochromatic insertions display distinct methylation signatures, reflecting the action of different epigenetic pathways. In conclusion, our results demonstrate that DNA methylation and alternative splicing are effective control mechanisms safeguarding the plant genome and transcriptome integrity after retrotransposition burst. Full article

(This article belongs to the Special Issue Repetitive DNA)

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19 pages, 3283 KB

Open AccessArticle

Evolution of ZW Sex Chromosomes in Ptyas Snakes (Reptilia, Colubridae): New Insights from a Molecular Cytogenetic Perspective

by Príncia Grejo Setti, Tariq Ezaz, Geize Aparecida Deon, Ricardo Utsunomia, Alongklod Tanomtong, Sukhonthip Ditcharoen, Nattasuda Donbundit, Montri Sumontha, Kriengkrai Seetapan, Phichaya Buasriyot, Krit Pinthong, Weera Thongnetr, Natália dos Santos, Fábio Porto-Foresti, Thomas Liehr and Marcelo de Bello Cioffi

Int. J. Mol. Sci. 2025, 26(10), 4540; https://doi.org/10.3390/ijms26104540 - 9 May 2025

Cited by 1 | Viewed by 1586

Abstract

Snakes are cytogenetically dynamic, characterized by largely conserved diploid chromosome numbers although displaying varied variable evolutionary stages of their sex chromosomes. This study examined four snakes, with a special focus on the genus Ptyas, to provide evolutionary insights into the evolution of ZW sex chromosomes. We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches, described for the first time the karyotype of Ptyas korros, and revisited the karyotype descriptions of P. mucosa, Chrysopelea ornata, and Fowlea flavipunctatus. We found that all species except F. flavipunctatus have highly heterochromatic W chromosomes enriched in satDNAs or microsatellite repeats. Repetitive sequences accumulate with the heterochromatinization of the W chromosome but are not necessarily associated with this process, demonstrating the dynamic makeup of snake sex chromosomes. Autosomal locus-specific and sex chromosome probes from Pogona vitticeps and Varanus acanthurus did not show hybridization signals in Ptyas snakes, suggesting divergent evolutionary pathways. This finding highlighted the dynamic nature of sex chromosome evolution in snakes, which occurred independently in lizards. Full article

(This article belongs to the Special Issue Repetitive DNA)

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Review

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23 pages, 1095 KB

Open AccessReview

Satellite DNA Genomics: The Ongoing Story

by Manuel A. Garrido-Ramos, Miroslav Plohl and Eva Šatović-Vukšić

Int. J. Mol. Sci. 2025, 26(23), 11291; https://doi.org/10.3390/ijms262311291 - 22 Nov 2025

Viewed by 293

Abstract

Tandemly repeated non-coding sequences, widely known as satellite DNAs (satDNAs), are extremely diverse and highly variable components of eukaryotic genomes. In recent years, advances in high-throughput sequencing and new bioinformatics platforms have enabled in-depth studies of all (or nearly all) tandem repeats in any genome (the satellitome), while a growing number of telomere-to-telomere assemblies facilitates their detailed mapping. Research performed on a large number of non-model plant and animal species changed significantly the “classical” view on these sequences, both in an organizational and functional sense, from ballast compacted in the form of heterochromatin to elements that are important for structuring the entire genome, as well as for its functions and evolution. The diversity of repeat families, and the complexity of their intraspecies and interspecies distribution patterns, posed new questions, urging for species-by-species comparative analyses. Here we integrate some basic features of different forms of sequences repeated in tandem and rapidly growing data evidencing extensive dispersal of satDNA sequences in euchromatin, their putative roles and evolutionary significance. Importantly, we also present and discuss various issues brought on by the use of new methodological approaches and point out potential threats to the analysis of satDNAs and satellitomes. Full article

(This article belongs to the Special Issue Repetitive DNA)

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18 pages, 1456 KB

Open AccessReview

Taxonomy, Phylogeny, Genomes, and Repeatomes in the Subgenera Salvia, Sclarea, and Glutinaria (Salvia, Lamiaceae)

by Julia V. Kalnyuk, Olga Yu. Yurkevich, Ekaterina D. Badaeva, Alexey R. Semenov, Svyatoslav A. Zoshchuk, Alexandra V. Amosova and Olga V. Muravenko

Int. J. Mol. Sci. 2025, 26(13), 6436; https://doi.org/10.3390/ijms26136436 - 4 Jul 2025

Cited by 4 | Viewed by 1190

Abstract

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

(This article belongs to the Special Issue Repetitive DNA)

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