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The Stability and Evolution of Genes and Genomes

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

Deadline for manuscript submissions: closed (20 August 2022) | Viewed by 31779

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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

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Keywords

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

Published Papers (13 papers)

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Editorial

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4 pages, 208 KiB

Open AccessEditorial

The Stability and Evolution of Genes and Genomes

by Luigi Viggiano and René Massimiliano Marsano

Genes 2023, 14(9), 1747; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14091747 - 31 Aug 2023

Viewed by 712

Abstract

The existence of current species can be attributed to a dynamic interplay between evolutionary forces and the maintenance of genetic information [...] Full article

(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)

Research

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17 pages, 2766 KiB

Open AccessArticle

Epigenetic Silencing of P-Element Reporter Genes Induced by Transcriptionally Active Domains of Constitutive Heterochromatin in Drosophila melanogaster

by Giovanni Messina, Emanuele Celauro, Renè Massimiliano Marsano, Yuri Prozzillo and Patrizio Dimitri

Genes 2023, 14(1), 12; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14010012 - 21 Dec 2022

Cited by 3 | Viewed by 1374

Abstract

Reporter genes inserted via P-element integration into different locations of the Drosophila melanogaster genome have been routinely used to monitor the functional state of chromatin domains. It is commonly thought that P-element-derived reporter genes are subjected to position effect variegation (PEV) when transposed into constitutive heterochromatin because they acquire heterochromatin-like epigenetic modifications that promote silencing. However, sequencing and annotation of the D. melanogaster genome have shown that constitutive heterochromatin is a genetically and molecularly heterogeneous compartment. In fact, in addition to repetitive DNAs, it harbors hundreds of functional genes, together accounting for a significant fraction of its entire genomic territory. Notably, most of these genes are actively transcribed in different developmental stages and tissues, irrespective of their location in heterochromatin. An open question in the genetic and molecular studies on PEV in D. melanogaster is whether functional heterochromatin domains, i.e., heterochromatin harboring active genes, are able to silence reporter genes therein transposed or, on the contrary, can drive their expression. In this work, we provide experimental evidence showing that strong silencing of the Pw⁺ reporters is induced even when they are integrated within or near actively transcribed loci in the pericentric regions of chromosome 2. Interestingly, some Pw⁺ reporters were found insensitive to the action of a known PEV suppressor. Two of them are inserted within Yeti, a gene expressed in the deep heterochromatin of chromosome 2 which carries active chromatin marks. The difference sensitivity to suppressors-exhibited Pw⁺ reporters supports the view that different epigenetic regulators or mechanisms control different regions of heterochromatin. Together, our results suggest that there may be more complexity regarding the molecular mechanisms underlying PEV. Full article

(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)

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19 pages, 2775 KiB

Open AccessArticle

Mosaic Evolution of Molecular Pathways for Sex Pheromone Communication in a Butterfly

by Caroline M. Nieberding, Patrícia Beldade, Véronique Baumlé, Gilles San Martin, Alok Arun, Georges Lognay, Nicolas Montagné, Lucie Bastin-Héline, Emmanuelle Jacquin-Joly, Céline Noirot, Christophe Klopp and Bertanne Visser

Genes 2022, 13(8), 1372; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13081372 - 31 Jul 2022

Cited by 1 | Viewed by 2197

Abstract

Unraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved ancestral traits and newly evolved derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~119 million years ago. In moths, it is the females that typically emit pheromones to attract male mates, but in butterflies males emit pheromones that are used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but they have remained relatively unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics to identify genes involved in the different steps (i.e., production, regulation, and reception) of sex pheromone communication of the butterfly Bicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulating sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale investigation of the genetic pathways underlying sex pheromone communication in a butterfly. Full article

(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)

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26 pages, 4142 KiB

Open AccessArticle

Was the Last Bacterial Common Ancestor a Monoderm after All?

by Raphaël R. Léonard, Eric Sauvage, Valérian Lupo, Amandine Perrin, Damien Sirjacobs, Paulette Charlier, Frédéric Kerff and Denis Baurain

Genes 2022, 13(2), 376; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13020376 - 18 Feb 2022

Cited by 5 | Viewed by 3502

Abstract

The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection. Full article

(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)

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15 pages, 1603 KiB

Open AccessArticle

The Ribosomal Protein RpL22 Interacts In Vitro with 5′-UTR Sequences Found in Some Drosophila melanogaster Transposons

by Crescenzio Francesco Minervini, Maria Francesca Berloco, René Massimiliano Marsano and Luigi Viggiano

Genes 2022, 13(2), 305; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13020305 - 05 Feb 2022

Cited by 2 | Viewed by 1800

Abstract

Mobility of eukaryotic transposable elements (TEs) are finely regulated to avoid an excessive mutational load caused by their movement. The transposition of retrotransposons is usually regulated through the interaction of host- and TE-encoded proteins, with non-coding regions (LTR and 5′-UTR) of the transposon. Examples of new potent cis-acting sequences, identified and characterized in the non-coding regions of retrotransposons, include the insulator of gypsy and Idefix, and the enhancer of ZAM of Drosophila melanogaster. Recently we have shown that in the 5′-UTR of the LTR-retrotransposon ZAM there is a sequence structured in tandem-repeat capable of operating as an insulator both in Drosophila (S2R⁺) and human cells (HEK293). Here, we test the hypothesis that tandem repeated 5′-UTR of a different LTR-retrotransposon could accommodate similar regulatory elements. The comparison of the 5′-UTR of some LTR-transposons allowed us to identify a shared motif of 13 bp, called Transposable Element Redundant Motif (TERM). Surprisingly, we demonstrated, by Yeast One-Hybrid assay, that TERM interacts with the D. melanogaster ribosomal protein RpL22. The Drosophila RpL22 has additional Ala-, Lys- and Pro-rich sequences at the amino terminus, which resembles the carboxy-terminal portion of histone H1 and histone H5. For this reason, it has been hypothesized that RpL22 might have two functions, namely the role in organizing the ribosome, and a potential regulatory role involving DNA-binding similar to histone H1, which represses transcription in Drosophila. In this paper, we show, by two independent sets of experiments, that DmRpL22 is able to directly and specifically bind DNA of Drosophila melanogaster. Full article

(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)

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17 pages, 1667 KiB

Open AccessArticle

Evidence of the Physical Interaction between Rpl22 and the Transposable Element Doc5, a Heterochromatic Transposon of Drosophila melanogaster

by Maria Francesca Berloco, Crescenzio Francesco Minervini, Roberta Moschetti, Antonio Palazzo, Luigi Viggiano and René Massimiliano Marsano

Genes 2021, 12(12), 1997; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12121997 - 16 Dec 2021

Cited by 5 | Viewed by 2225

Abstract

Chromatin is a highly dynamic biological entity that allows for both the control of gene expression and the stabilization of chromosomal domains. Given the high degree of plasticity observed in model and non-model organisms, it is not surprising that new chromatin components are frequently described. In this work, we tested the hypothesis that the remnants of the Doc5 transposable element, which retains a heterochromatin insertion pattern in the melanogaster species complex, can be bound by chromatin proteins, and thus be involved in the organization of heterochromatic domains. Using the Yeast One Hybrid approach, we found Rpl22 as a potential interacting protein of Doc5. We further tested in vitro the observed interaction through Electrophoretic Mobility Shift Assay, uncovering that the N-terminal portion of the protein is sufficient to interact with Doc5. However, in situ localization of the native protein failed to detect Rpl22 association with chromatin. The results obtained are discussed in the light of the current knowledge on the extra-ribosomal role of ribosomal protein in eukaryotes, which suggests a possible role of Rpl22 in the determination of the heterochromatin in Drosophila. Full article

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17 pages, 6087 KiB

Open AccessArticle

New Data on Comparative Cytogenetics of the Mouse-Like Hamsters (Calomyscus Thomas, 1905) from Iran and Turkmenistan

by Svetlana A. Romanenko, Vladimir G. Malikov, Ahmad Mahmoudi, Feodor N. Golenishchev, Natalya A. Lemskaya, Jorge C. Pereira, Vladimir A. Trifonov, Natalia A. Serdyukova, Malcolm A. Ferguson-Smith, Mansour Aliabadian and Alexander S. Graphodatsky

Genes 2021, 12(7), 964; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12070964 - 24 Jun 2021

Cited by 8 | Viewed by 2239

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 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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10 pages, 1120 KiB

Open AccessArticle

Evolution of Oxidative Phosphorylation (OXPHOS) Genes Reflecting the Evolutionary and Life Histories of Fig Wasps (Hymenoptera, Chalcidoidea)

by Yi Zhou, Dawei Huang, Zhaozhe Xin and Jinhua Xiao

Genes 2020, 11(11), 1353; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11111353 - 15 Nov 2020

Cited by 4 | Viewed by 1910

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 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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16 pages, 906 KiB

Open AccessReview

Leukocyte Telomere Length as a Molecular Biomarker of Coronary Heart Disease

by Olga V. Zimnitskaya, Marina M. Petrova, Natalia V. Lareva, Marina S. Cherniaeva, Mustafa Al-Zamil, Anastasia E. Ivanova and Natalia A. Shnayder

Genes 2022, 13(7), 1234; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13071234 - 12 Jul 2022

Cited by 7 | Viewed by 2758

Abstract

Background. This work is a review of preclinical and clinical studies of the role of telomeres and telomerase in the development and progression of coronary heart disease (CHD). Materials and methods. A search for full-text publications (articles, reviews, meta-analyses, Cochrane reviews, and clinical cases) in English and Russian was carried out in the databases PubMed, Oxford University Press, Scopus, Web of Science, Springer, and E-library electronic library using keywords and their combinations. The search depth is 11 years (2010–2021). Results. The review suggests that the relative leukocyte telomere length (LTL) is associated with the development of socially significant and widespread cardiovascular diseases such as CHD and essential hypertension. At the same time, the interests of researchers are mainly focused on the study of the relative LTL in CHD. Conclusions. Despite the scientific and clinical significance of the analyzed studies of the relative length of human LTL as a biological marker of cardiovascular diseases, their implementation in real clinical practice is difficult due to differences in the design and methodology of the analyzed studies, as well as differences in the samples by gender, age, race, and ethnicity. The authors believe that clinical studies of the role of the relative length of leukocyte telomeres in adult patients with coronary heart disease are the most promising and require large multicenter studies with a unified design and methodology. Full article

(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)

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34 pages, 510 KiB

Open AccessReview

Saccharomyces cerevisiae as a Tool for Studying Mutations in Nuclear Genes Involved in Diseases Caused by Mitochondrial DNA Instability

by Alexandru Ionut Gilea, Camilla Ceccatelli Berti, Martina Magistrati, Giulia di Punzio, Paola Goffrini, Enrico Baruffini and Cristina Dallabona

Genes 2021, 12(12), 1866; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12121866 - 24 Nov 2021

Cited by 11 | Viewed by 3057

Abstract

Mitochondrial DNA (mtDNA) maintenance is critical for oxidative phosphorylation (OXPHOS) since some subunits of the respiratory chain complexes are mitochondrially encoded. Pathological mutations in nuclear genes involved in the mtDNA metabolism may result in a quantitative decrease in mtDNA levels, referred to as mtDNA depletion, or in qualitative defects in mtDNA, especially in multiple deletions. Since, in the last decade, most of the novel mutations have been identified through whole-exome sequencing, it is crucial to confirm the pathogenicity by functional analysis in the appropriate model systems. Among these, the yeast Saccharomyces cerevisiae has proved to be a good model for studying mutations associated with mtDNA instability. This review focuses on the use of yeast for evaluating the pathogenicity of mutations in six genes, MPV17/SYM1, MRM2/MRM2, OPA1/MGM1, POLG/MIP1, RRM2B/RNR2, and SLC25A4/AAC2, all associated with mtDNA depletion or multiple deletions. We highlight the techniques used to construct a specific model and to measure the mtDNA instability as well as the main results obtained. We then report the contribution that yeast has given in understanding the pathogenic mechanisms of the mutant variants, in finding the genetic suppressors of the mitochondrial defects and in the discovery of molecules able to improve the mtDNA stability. Full article

(This article belongs to the Special Issue The Stability and Evolution of Genes and Genomes)

14 pages, 4903 KiB

Open AccessReview

The Evolutionary Relevance of Social Learning and Transmission in Non-Social Arthropods with a Focus on Oviposition-Related Behaviors

by Caroline M. Nieberding, Matteo Marcantonio, Raluca Voda, Thomas Enriquez and Bertanne Visser

Genes 2021, 12(10), 1466; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101466 - 22 Sep 2021

Cited by 4 | Viewed by 2727

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 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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25 pages, 2508 KiB

Open AccessReview

Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review

by Angelo Pavesi

Genes 2021, 12(6), 809; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060809 - 26 May 2021

Cited by 16 | Viewed by 3734

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 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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7 pages, 1442 KiB

Open AccessReview

The Adenine/Thymine Deleterious Selection Model for GC Content Evolution at the Third Codon Position of the Histone Genes in Drosophila

by Yoshinori Matsuo

Genes 2021, 12(5), 721; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12050721 - 12 May 2021

Cited by 3 | Viewed by 2000

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 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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