Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
9.0
4.9
Journals
IJMS
Special Issues
Repetitive DNA
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Repetitive DNA

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: 30 October 2025 | Viewed by 3361

Special Issue Editors

Dr. Eva Šatović-Vukšić

E-Mail Website
Guest Editor
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
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Miroslav Plohl

E-Mail Website
Guest Editor
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
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Manuel A. Garrido-Ramos

E-Mail Website
Guest Editor
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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

18 pages, 2910 KiB  
Article
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
Viewed by 428
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

25 pages, 9238 KiB  
Article
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
Viewed by 1107
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

19 pages, 3283 KiB  
Article
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
Viewed by 1131
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

Review

Jump to: Research

18 pages, 1456 KiB  
Review
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
Viewed by 263
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 [...] Read more.
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)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop