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New Insights on Vertebrate Repetitive DNA
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New Insights on Vertebrate 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: 20 December 2024 | Viewed by 9225

Special Issue Editors

Dr. Maria Assunta Biscotti

E-Mail Website
Guest Editor
Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
Interests: genome evolution; repetitive DNA; transposable elements; gene families; genomic and transcriptomic data; evolutionary biology
Special Issues, Collections and Topics in MDPI journals
Dr. Marco Barucca

E-Mail Website
Guest Editor
Dipartimento di Scienze della Vita e Dell’Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: genome evolution; repetitive DNA; transposable elements; gene families; genomic and transcriptomic data; evolutionary genetics
Special Issues, Collections and Topics in MDPI journals
Dr. Federica Carducci

E-Mail Website
Guest Editor
Laboratory of Evolutionary Genetics, Department of Life and Environmental Sciences (DiSVA), Polytechnic University of Marche, Via Brecce Bianche, I-60131 Ancona, Italy
Interests: genome evolution; transposable elements; gene families; genomic and transcriptomic data; evolutionary genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Repetitive DNA has attracted the interest of evolutionary biologists. It constitutes the major proportion of all nuclear DNA in most eukaryotic genomes. The significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles. The advent of next-generation sequencing technologies has strongly contributed to insights on the evolutionary meaning of repetitive DNA. However, many questions are open about the origin, evolutionary mode, and functions that repetitive sequences might have in the genome and how these elements are controlled and positively used by the host genome to gain evolutionary advantages.

In this Special Issue of International Journal of Molecular Sciences, we invite researchers from all over the world to share advances in our understanding of the role of the main types of repetitive DNA (transposable elements and satellite DNA) in vertebrate genomes.

Dr. Maria Assunta Biscotti
Dr. Marco Barucca
Dr. Federica Carducci
Guest Editors

Manuscript Submission Information

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Keywords

  • transposable elements
  • transposable element activity
  • transposable element silencing mechanisms
  • satellite DNA
  • repetitive DNA

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Published Papers (5 papers)

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Research

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15 pages, 2937 KiB  
Article
Novel Concept of Alpha Satellite Cascading Higher-Order Repeats (HORs) and Precise Identification of 15mer and 20mer Cascading HORs in Complete T2T-CHM13 Assembly of Human Chromosome 15
by Matko Glunčić, Ines Vlahović, Marija Rosandić and Vladimir Paar
Int. J. Mol. Sci. 2024, 25(8), 4395; https://doi.org/10.3390/ijms25084395 - 16 Apr 2024
Cited by 1 | Viewed by 1304
Abstract
Unraveling the intricate centromere structure of human chromosomes holds profound implications, illuminating fundamental genetic mechanisms and potentially advancing our comprehension of genetic disorders and therapeutic interventions. This study rigorously identified and structurally analyzed alpha satellite higher-order repeats (HORs) within the centromere of human [...] Read more.
Unraveling the intricate centromere structure of human chromosomes holds profound implications, illuminating fundamental genetic mechanisms and potentially advancing our comprehension of genetic disorders and therapeutic interventions. This study rigorously identified and structurally analyzed alpha satellite higher-order repeats (HORs) within the centromere of human chromosome 15 in the complete T2T-CHM13 assembly using the high-precision GRM2023 algorithm. The most extensive alpha satellite HOR array in chromosome 15 reveals a novel cascading HOR, housing 429 15mer HOR copies, containing 4-, 7- and 11-monomer subfragments. Within each row of cascading HORs, all alpha satellite monomers are of distinct types, as in regular Willard’s HORs. However, different HOR copies within the same cascading 15mer HOR contain more than one monomer of the same type. Each canonical 15mer HOR copy comprises 15 monomers belonging to only 9 different monomer types. Notably, 65% of the 429 15mer cascading HOR copies exhibit canonical structures, while 35% display variant configurations. Identified as the second most extensive alpha satellite HOR, another novel cascading HOR within human chromosome 15 encompasses 164 20mer HOR copies, each featuring two subfragments. Moreover, a distinct pattern emerges as interspersed 25mer/26mer structures differing from regular Willard’s HORs and giving rise to a 34-monomer subfragment. Only a minor 18mer HOR array of 12 HOR copies is of the regular Willard’s type. These revelations highlight the complexity within the chromosome 15 centromeric region, accentuating deviations from anticipated highly regular patterns and hinting at profound information encoding and functional potential within the human centromere. Full article
(This article belongs to the Special Issue New Insights on Vertebrate Repetitive DNA)
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14 pages, 3803 KiB  
Article
Mechanisms of Karyotypic Diversification in Ancistrus (Siluriformes, Loricariidae): Inferences from Repetitive Sequence Analysis
by Kevin Santos da Silva, Larissa Glugoski, Marcelo Ricardo Vicari, Augusto César Paes de Souza, Alberto Akama, Julio Cesar Pieczarka and Cleusa Yoshiko Nagamachi
Int. J. Mol. Sci. 2023, 24(18), 14159; https://doi.org/10.3390/ijms241814159 - 15 Sep 2023
Viewed by 1187
Abstract
Ancistrus is a highly diverse neotropical fish genus that exhibits extensive chromosomal variability, encompassing karyotypic morphology, diploid chromosome number (2n = 34–54), and the evolution of various types of sex chromosome systems. Robertsonian rearrangements related to unstable chromosomal sites are here described. Here, [...] Read more.
Ancistrus is a highly diverse neotropical fish genus that exhibits extensive chromosomal variability, encompassing karyotypic morphology, diploid chromosome number (2n = 34–54), and the evolution of various types of sex chromosome systems. Robertsonian rearrangements related to unstable chromosomal sites are here described. Here, the karyotypes of two Ancistrus species were comparatively analyzed using classical cytogenetic techniques, in addition to isolation, cloning, sequencing, molecular characterization, and fluorescence in situ hybridization of repetitive sequences (i.e., 18S and 5S rDNA; U1, U2, and U5 snDNA; and telomere sequences). The species analyzed here have different karyotypes: Ancistrus sp. 1 (2n = 38, XX/XY) and Ancistrus cirrhosus (2n = 34, no heteromorphic sex chromosomes). Comparative mapping showed different organizations for the analyzed repetitive sequences: 18S and U1 sequences occurred in a single site in all populations of the analyzed species, while 5S and U2 sequences could occur in single or multiple sites. A sequencing analysis confirmed the identities of the U1, U2, and U5 snDNA sequences. Additionally, a syntenic condition for U2-U5 snDNA was found in Ancistrus. In a comparative analysis, the sequences of rDNA and U snDNA showed inter- and intraspecific chromosomal diversification. The occurrence of Robertsonian rearrangements and other dispersal mechanisms of repetitive sequences are discussed. Full article
(This article belongs to the Special Issue New Insights on Vertebrate Repetitive DNA)
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17 pages, 2781 KiB  
Article
Cytogenetics Meets Genomics: Cytotaxonomy and Genomic Relationships among Color Variants of the Asian Arowana Scleropages formosus
by Gustavo A. Toma, Natália dos Santos, Rodrigo dos Santos, Petr Rab, Rafael Kretschmer, Tariq Ezaz, Luiz A. C. Bertollo, Thomas Liehr, Fábio Porto-Foresti, Terumi Hatanaka, Alongklod Tanomtong, Ricardo Utsunomia and Marcelo B. Cioffi
Int. J. Mol. Sci. 2023, 24(10), 9005; https://doi.org/10.3390/ijms24109005 - 19 May 2023
Cited by 5 | Viewed by 2050
Abstract
Scleropages formosus (Osteoglossiformes, Teleostei) represents one of the most valued ornamental fishes, yet it is critically endangered due to overexploitation and habitat destruction. This species encompasses three major color groups that naturally occur in allopatric populations, but the evolutionary and taxonomic relationships of [...] Read more.
Scleropages formosus (Osteoglossiformes, Teleostei) represents one of the most valued ornamental fishes, yet it is critically endangered due to overexploitation and habitat destruction. This species encompasses three major color groups that naturally occur in allopatric populations, but the evolutionary and taxonomic relationships of S. formosus color varieties remain uncertain. Here, we utilized a range of molecular cytogenetic techniques to characterize the karyotypes of five S. formosus color phenotypes, which correspond to naturally occurring variants: the red ones (Super Red); the golden ones (Golden Crossback and Highback Golden); the green ones (Asian Green and Yellow Tail Silver). Additionally, we describe the satellitome of S. formosus (Highback Golden) by applying a high-throughput sequencing technology. All color phenotypes possessed the same karyotype structure 2n = 50 (8m/sm + 42st/a) and distribution of SatDNAs, but different chromosomal locations of rDNAs, which were involved in a chromosome size polymorphism. Our results show indications of population genetic structure and microstructure differences in karyotypes of the color phenotypes. However, the findings do not clearly back up the hypothesis that there are discrete lineages or evolutionary units among the color phenotypes of S. formosus, but another case of interspecific chromosome stasis cannot be excluded. Full article
(This article belongs to the Special Issue New Insights on Vertebrate Repetitive DNA)
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12 pages, 3082 KiB  
Article
LTR Retroelements and Bird Adaptation to Arid Environments
by Elisa Carotti, Edith Tittarelli, Adriana Canapa, Maria Assunta Biscotti, Federica Carducci and Marco Barucca
Int. J. Mol. Sci. 2023, 24(7), 6332; https://doi.org/10.3390/ijms24076332 - 28 Mar 2023
Cited by 1 | Viewed by 1889
Abstract
TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a [...] Read more.
TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a possible relationship between the amount of specific TE types and environmental changes that characterized the Oligocene era in Australia. Therefore, the mobilome of 29 bird species, belonging to a total of 11 orders, was analyzed. Our results confirmed that LINE retroelements are not predominant in all species of this evolutionary lineage and highlighted an LTR retroelement dominance in species with an Australian-related evolutionary history. The bird LTR retroelement expansion might have happened in response to the Earth’s dramatic climate changes that occurred about 30 Mya, followed by a progressive aridification across most of Australian landmasses. Therefore, in birds, LTR retroelement burst might have represented an evolutionary advantage in the adaptation to arid/drought environments. Full article
(This article belongs to the Special Issue New Insights on Vertebrate Repetitive DNA)
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Review

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16 pages, 2360 KiB  
Review
Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin
by Elisa Carotti, Federica Carducci, Marco Barucca, Adriana Canapa and Maria Assunta Biscotti
Int. J. Mol. Sci. 2023, 24(14), 11591; https://doi.org/10.3390/ijms241411591 - 18 Jul 2023
Viewed by 2226
Abstract
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for [...] Read more.
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements. Full article
(This article belongs to the Special Issue New Insights on Vertebrate Repetitive DNA)
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