Special Issue "The Stability and Evolution of Genes and Genomes"

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

Deadline for manuscript submissions: 20 March 2022.

Special Issue Editors

Dr. Luigi Viggiano
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Guest Editor
Department of Biology, University of Bari, Bari (70125), Italy
Interests: evolution; epigenetics; HGT; stem cells; neurodegenerative disorder
Dr. Renè Massimiliano Marsano
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Guest Editor
Department of Biology, University of Bari, Bari (70125), Italy
Interests: transposable elements; heterochromatin; evolution; Gene Expression; horizontal transposon transfer, mitochondrial biogenesis

Special Issue Information

Dear Colleagues,

Extant species are the result of an arms race between evolutionary processes and the stabilization of the genetic information. A plethora of mechanisms can contribute to the evolution of genes and genomes including mutations, indels, CNVs, chromosomal rearrangements, horizontal gene transfer, and transposition. On the other side, cellular mechanisms that counterbalance excessive variation contribute to the stability of genes and genomes and preserve the faithful pass down of the genetic material from generation to generation. These latter mechanisms include DNA damage surveillance, DNA repair mechanisms, mitotic and meiotic checkpoints, and epigenetic organization of centromeres and telomeres.

In this Special Issue, we aim to collect original research papers and reviews to address the complex dynamics underlying these two contrasting processes using molecular evolution, population genetic, and functional genomic approaches in model and non-model organisms.

Dr. Luigi Viggiano
Dr. Renè Massimiliano Marsano
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 papers will be 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 2000 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

  • Gene and Genome Evolution 
  • Horizontal Transfer 
  • Transposable Elements 
  • CNV 
  • Mutations 
  • Adaptation 
  • Euchromatin and Heterochromatin 
  • Epigenetics 
  • Chromosome Structure and Stability 
  • Genome Surveillance

Published Papers (5 papers)

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Research

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Article
New Data on Comparative Cytogenetics of the Mouse-Like Hamsters (Calomyscus Thomas, 1905) from Iran and Turkmenistan
Genes 2021, 12(7), 964; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12070964 - 24 Jun 2021
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Abstract
The taxonomy of the genus Calomyscus remains controversial. According to the latest systematics the genus includes eight species with great karyotypic variation. Here, we studied karyotypes of 14 Calomyscus individuals from different regions of Iran and Turkmenistan using a new set of chromosome [...] Read more.
The taxonomy of the genus Calomyscus remains controversial. According to the latest systematics the genus includes eight species with great karyotypic variation. Here, we studied karyotypes of 14 Calomyscus individuals from different regions of Iran and Turkmenistan using a new set of chromosome painting probes from a Calomyscus sp. male (2n = 46, XY; Shahr-e-Kord-Soreshjan-Cheshme Maiak Province). We showed the retention of large syntenic blocks in karyotypes of individuals with identical chromosome numbers. The only rearrangement (fusion 2/21) differentiated Calomyscus elburzensis, Calomyscus mystax mystax, and Calomyscus sp. from Isfahan Province with 2n = 44 from karyotypes of C. bailwardi, Calomyscus sp. from Shahr-e-Kord, Chahar Mahal and Bakhtiari-Aloni, and Khuzestan-Izeh Provinces with 2n = 46. The individuals from Shahdad tunnel, Kerman Province with 2n = 51–52 demonstrated non-centric fissions of chromosomes 4, 5, and 6 of the 46-chromosomal form with the formation of separate small acrocentrics. A heteromorphic pair of chromosomes in a specimen with 2n = 51 resulted from a fusion of two autosomes. C-banding and chromomycin A3-DAPI staining after G-banding showed extensive heterochromatin variation between individuals. Full article
(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)
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Article
Evolution of Oxidative Phosphorylation (OXPHOS) Genes Reflecting the Evolutionary and Life Histories of Fig Wasps (Hymenoptera, Chalcidoidea)
Genes 2020, 11(11), 1353; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11111353 - 15 Nov 2020
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Abstract
Fig wasps are a peculiar group of insects which, for millions of years, have inhabited the enclosed syconia of fig trees. Considering the relatively closed and dark environment of fig syconia, we hypothesize that the fig wasps’ oxidative phosphorylation (OXPHOS) pathway, which is [...] Read more.
Fig wasps are a peculiar group of insects which, for millions of years, have inhabited the enclosed syconia of fig trees. Considering the relatively closed and dark environment of fig syconia, we hypothesize that the fig wasps’ oxidative phosphorylation (OXPHOS) pathway, which is the main oxygen consumption and adenosine triphosphate (ATP) production system, may have adaptively evolved. In this study, we manually annotated the OXPHOS genes of 11 species of fig wasps, and compared the evolutionary patterns of OXPHOS genes for six pollinators and five non-pollinators. Thirteen mitochondrial protein-coding genes and 30 nuclear-coding single-copy orthologous genes were used to analyze the amino acid substitution rate and natural selection. The results showed high amino acid substitution rates of both mitochondrial and nuclear OXPHOS genes in fig wasps, implying the co-evolution of mitochondrial and nuclear genes. Our results further revealed that the OXPHOS-related genes evolved significantly faster in pollinators than in non-pollinators, and five genes had significant positive selection signals in the pollinator lineage, indicating that OXPHOS genes play an important role in the adaptation of pollinators. This study can help us understand the relationship between gene evolution and environmental adaptation. Full article
(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)
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Review

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Review
The Evolutionary Relevance of Social Learning and Transmission in Non-Social Arthropods with a Focus on Oviposition-Related Behaviors
Genes 2021, 12(10), 1466; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101466 - 22 Sep 2021
Viewed by 467
Abstract
Research on social learning has centered around vertebrates, but evidence is accumulating that small-brained, non-social arthropods also learn from others. Social learning can lead to social inheritance when socially acquired behaviors are transmitted to subsequent generations. Using oviposition site selection, a critical behavior [...] Read more.
Research on social learning has centered around vertebrates, but evidence is accumulating that small-brained, non-social arthropods also learn from others. Social learning can lead to social inheritance when socially acquired behaviors are transmitted to subsequent generations. Using oviposition site selection, a critical behavior for most arthropods, as an example, we first highlight the complementarities between social and classical genetic inheritance. We then discuss the relevance of studying social learning and transmission in non-social arthropods and document known cases in the literature, including examples of social learning from con- and hetero-specifics. We further highlight under which conditions social learning can be adaptive or not. We conclude that non-social arthropods and the study of oviposition behavior offer unparalleled opportunities to unravel the importance of social learning and inheritance for animal evolution. Full article
(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)
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Review
Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review
Genes 2021, 12(6), 809; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060809 - 26 May 2021
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Abstract
During their long evolutionary history viruses generated many proteins de novo by a mechanism called “overprinting”. Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open [...] Read more.
During their long evolutionary history viruses generated many proteins de novo by a mechanism called “overprinting”. Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open reading frame (ORF). Overlapping genes represent an intriguing example of adaptive conflict, because they simultaneously encode two proteins whose freedom to change is constrained by each other. However, overlapping genes are also a source of genetic novelties, as the constraints under which alternative ORFs evolve can give rise to proteins with unusual sequence properties, most importantly the potential for novel functions. Starting with the discovery of overlapping genes in phages infecting Escherichia coli, this review covers a range of studies dealing with detection of overlapping genes in small eukaryotic viruses (genomic length below 30 kb) and recognition of their critical role in the evolution of pathogenicity. Origin of overlapping genes, what factors favor their birth and retention, and how they manage their inherent adaptive conflict are extensively reviewed. Special attention is paid to the assembly of overlapping genes into ad hoc databases, suitable for future studies, and to the development of statistical methods for exploring viral genome sequences in search of undiscovered overlaps. Full article
(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)
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Review
The Adenine/Thymine Deleterious Selection Model for GC Content Evolution at the Third Codon Position of the Histone Genes in Drosophila
Genes 2021, 12(5), 721; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12050721 - 12 May 2021
Viewed by 550
Abstract
The evolution of the GC (guanine cytosine) content at the third codon position of the histone genes (H1, H2A, H2B, H3, H4, H2AvD, H3.3A, H3.3B, and H4r) in 12 or more Drosophila species [...] Read more.
The evolution of the GC (guanine cytosine) content at the third codon position of the histone genes (H1, H2A, H2B, H3, H4, H2AvD, H3.3A, H3.3B, and H4r) in 12 or more Drosophila species is reviewed. For explaining the evolution of the GC content at the third codon position of the genes, a model assuming selection with a deleterious effect for adenine/thymine and a size effect is presented. The applicability of the model to whole-genome genes is also discussed. Full article
(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)
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