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Genome Evolution
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Genome Evolution

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 15 May 2024 | Viewed by 5034

Special Issue Editors

Dr. Eva Šatović-Vukšić

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Guest Editor
Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
Interests: satellite DNA; mobile elements; heterochromatin; bivalves; NGS; satellitome; repeatome; genome biology; genome evolution
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Miroslav Plohl

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Guest Editor
Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
Interests: repetitive DNA sequences; satellite DNA; mobile elements; heterochromatin; centromere; chromosome; genome evolution
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Manuel A. Garrido-Ramos

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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,

Changes on a genome level represent the powerful force that drives the evolution of the living world, resulting in its extreme complexity, resilience and diversity, existing in myriads of forms and changing over time. A significant contribution to the evolution of genomes are changes in their DNA landscapes, with repetitive DNA sequences being major players. Large genome fractions are composed of mobile elements and sequences repeated in tandem (satellite DNAs), often closely interlinked in sequence, mechanisms of dispersal, and chromosomal locations. Their individual and total contribution is highly divergent among species, also affecting the heterochromatin/euchromatin distribution, centromere positioning, and the genome size. The consequence of their evolutionary dynamics can result in small-scale and large-scale genome rearrangements, heterochromatin heteromorphism, alterations in chromosomal architecture and number, and ultimately, in hybridization compatibility. Recent high-throughput methodologies have enabled comparisons of comprehensive inventories of repetitive DNAs, improved assemblies of repeat rich regions and detailed mapping, the chromatin-immunoprecipitation-based characterization of DNA sequences from different chromatin forms, as well as analyses of repetitive DNA transcripts. These methodologies, paired with cytogenetic experiments, phylogenetic analyses, and crosstalks between different “omics”, are of great help in elucidating the mechanisms that can explain the roles and evolution of repetitive sequences and genomes as a whole. We would therefore like to invite submissions of original research or review articles on any topic addressing questions of repetitive and other types of DNA sequences, chromatin components, mechanisms and processes able to change genome architecture and drive its 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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • genome/chromosome evolution
  • genome/chromosome architecture
  • genome organization
  • genome size
  • heterochromatin
  • euchromatin
  • centromere
  • repetitive DNA structure
  • function and evolution
  • satellitome
  • repeatome
  • cytogenomics
  • phylogenetics

Published Papers (2 papers)

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Review

18 pages, 1498 KiB  
Review
Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction
by Desiree Brancato, Elvira Coniglio, Francesca Bruno, Vincenzo Agostini, Salvatore Saccone and Concetta Federico
Genes 2023, 14(8), 1604; https://doi.org/10.3390/genes14081604 - 10 Aug 2023
Cited by 3 | Viewed by 2995
Abstract
In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, [...] Read more.
In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction. Full article
(This article belongs to the Special Issue Genome Evolution)
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18 pages, 1438 KiB  
Review
EMAST Type of Microsatellite Instability—A Distinct Entity or Blurred Overlap between Stable and MSI Tumors
by Kristina Vuković Đerfi, Anamarija Salar, Tamara Cacev and Sanja Kapitanović
Genes 2023, 14(7), 1474; https://doi.org/10.3390/genes14071474 - 19 Jul 2023
Cited by 1 | Viewed by 1639
Abstract
Microsatellite instability (MSI) represents an accumulation of frameshifts in short tandem repeats, microsatellites, across the genome due to defective DNA mismatch repair (dMMR). MSI has been associated with distinct clinical, histological, and molecular features of tumors and has proven its prognostic and therapeutic [...] Read more.
Microsatellite instability (MSI) represents an accumulation of frameshifts in short tandem repeats, microsatellites, across the genome due to defective DNA mismatch repair (dMMR). MSI has been associated with distinct clinical, histological, and molecular features of tumors and has proven its prognostic and therapeutic value in different types of cancer. Recently, another type of microsatellite instability named elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) has been reported across many different tumors. EMAST tumors have been associated with chronic inflammation, higher tumor stage, and poor prognosis. Nevertheless, the clinical significance of EMAST and its relation to MSI remains unclear. It has been proposed that EMAST arises as a result of isolated MSH3 dysfunction or as a secondary event in MSI tumors. Even though previous studies have associated EMAST with MSI-low phenotype in tumors, recent studies show a certain degree of overlap between EMAST and MSI-high tumors. However, even in stable tumors, (MSS) frameshifts in microsatellites can be detected as a purely stochastic event, raising the question of whether EMAST truly represents a distinct type of microsatellite instability. Moreover, a significant fraction of patients with MSI tumors do not respond to immunotherapy and it can be speculated that in these tumors, EMAST might act as a modifying factor. Full article
(This article belongs to the Special Issue Genome Evolution)
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