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Nucleotide Sequences and Genome Organization
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Nucleotide Sequences and Genome Organization

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

Deadline for manuscript submissions: closed (30 April 2021) | Viewed by 26751

Special Issue Editor

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,

Nowadays, it is possible to sequence large and complex eukaryotic genomes in a short time at a relatively competitive cost, even though only 50 years have passed since the challenging initial attempts at obtaining the first nucleotide sequences from small viral genomes. Notwithstanding, the knowledge acquired on genome organization has increased enormously during these past few years. During this time, technologies previously considered inconceivable have been developed, databases for nucleotide sequences that grow continuously were generated, and new disciplines such as Computational Biology and Genomics have been conceived. Moreover, we have learnt how complex eukaryotic genomes are. Genome complexity refers to genes and to their regulatory elements in addition to the wide diversity of repetitive elements that have made a great impact on the organization, function, and evolution of genomes.

We would like to invite submissions of original research or review articles on any topic related to “Nucleotide Sequences and Genome Organization”. This Special Issue addresses all kinds of research related to our current knowledge on the organization of eukaryotic genomes from a functional and evolutionary perspective. We look forward to receiving your contributions.

Prof. Manuel A. Garrido-Ramos
Guest Editor

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

  • Genomics
  • Computational biology
  • Evolutionary genomics
  • SNPs
  • Multigene families
  • Non-coding DNA
  • Centromeres
  • Telomeres
  • Transposable elements
  • Satellite DNA
  • Mitogenomes
  • Plastomes

Published Papers (7 papers)

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Research

Jump to: Review

15 pages, 2637 KiB  
Article
Expanding the Search for Sperm Transmission Elements in the Mitochondrial Genomes of Bivalve Mollusks
by Donald T. Stewart, Brent M. Robicheau, Noor Youssef, Manuel A. Garrido-Ramos, Emily E. Chase and Sophie Breton
Genes 2021, 12(8), 1211; https://doi.org/10.3390/genes12081211 - 05 Aug 2021
Cited by 3 | Viewed by 2186
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) in bivalve mollusks is one of the most notable departures from the paradigm of strict maternal inheritance of mtDNA among metazoans. Recently, work on the Mediterranean mussel Mytilus galloprovincialis suggested that a nucleotide motif in [...] Read more.
Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) in bivalve mollusks is one of the most notable departures from the paradigm of strict maternal inheritance of mtDNA among metazoans. Recently, work on the Mediterranean mussel Mytilus galloprovincialis suggested that a nucleotide motif in the control region of this species, known as the sperm transmission element (STE), helps protect male-transmitted mitochondria from destruction during spermatogenesis. Subsequent studies found similar, yet divergent, STE motifs in other marine mussels. Here, we extend the in silico search for mtDNA signatures resembling known STEs. This search is carried out for the large unassigned regions of 157 complete mitochondrial genomes from within the Mytiloida, Veneroida, Unionoida, and Ostreoida bivalve orders. Based on a sliding window approach, we present evidence that there are additional putative STE signatures in the large unassigned regions of several marine clams and freshwater mussels with DUI. We discuss the implications of this finding for interpreting the origin of doubly uniparental inheritance in ancestral bivalve mollusks, as well as potential future in vitro and in silico studies that could further refine our understanding of the early evolution of this unusual system of mtDNA inheritance. Full article
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
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10 pages, 1444 KiB  
Article
Gene Conversion amongst Alu SINE Elements
by Liliya Doronina, Olga Reising and Jürgen Schmitz
Genes 2021, 12(6), 905; https://doi.org/10.3390/genes12060905 - 11 Jun 2021
Cited by 5 | Viewed by 2667
Abstract
The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted evolution is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions [...] Read more.
The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted evolution is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions of the converted genes. Transposed elements (TE), especially Alu short interspersed elements (SINE) that have more than a million copies in primate genomes, are a significant source of homologous units and a verified target of gene conversion. The consequences of such a recombination-based process are diverse, including multiplications of functional TE internal binding domains and, for evolutionists, confusing divergent annotations of orthologous transposable elements in related species. We systematically extracted and compared 68,097 Alu insertions in various primates looking for potential events of TE gene conversion and discovered 98 clear cases of Alu–Alu gene conversion, including 64 cases for which the direction of conversion was identified (e.g., AluS conversion to AluY). Gene conversion also does not necessarily affect the entire homologous sequence, and we detected 69 cases of partial gene conversion that resulted in virtual hybrids of two elements. Phylogenetic screening of gene-converted Alus revealed three clear hotspots of the process in the ancestors of Catarrhini, Hominoidea, and gibbons. In general, our systematic screening of orthologous primate loci for gene-converted TEs provides a new strategy and view of a post-integrative process that changes the identities of such elements. Full article
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
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13 pages, 2857 KiB  
Article
High Genetic Diversity despite Conserved Karyotype Organization in the Giant Trahiras from Genus Hoplias (Characiformes, Erythrinidae)
by Francisco de M. C. Sassi, Manolo F. Perez, Vanessa Cristina S. Oliveira, Geize A. Deon, Fernando H. S. de Souza, Pedro H. N. Ferreira, Ezequiel A. de Oliveira, Terumi Hatanaka, Thomas Liehr, Luiz A. C. Bertollo and Marcelo de B. Cioffi
Genes 2021, 12(2), 252; https://doi.org/10.3390/genes12020252 - 10 Feb 2021
Cited by 4 | Viewed by 3601
Abstract
In the fish genus Hoplias, two major general groups can be found, one of which is formed by the “common trahiras” (Hoplias malabaricus group) and the other by the “giant trahiras” (Hoplias lacerdae group, in addition to Hoplias aimara), [...] Read more.
In the fish genus Hoplias, two major general groups can be found, one of which is formed by the “common trahiras” (Hoplias malabaricus group) and the other by the “giant trahiras” (Hoplias lacerdae group, in addition to Hoplias aimara), which usually comprises specimens of larger body size. Previous investigations from the giant trahiras group recovered 2n = 50 meta/submetacentric chromosomes and no sex chromosome differentiation, indicating a probable conservative pattern for their karyotype organization. Here, we conducted comparative cytogenetic studies in six giant trahiras species, two of them for the first time. We employed standard and advanced molecular cytogenetics procedures, including comparative genomic hybridization (CGH), as well as genomic assessments of diversity levels and phylogenetic relationships among them. The results strongly suggest that the giant trahiras have a particular and differentiated evolutionary pathway inside the Hoplias genus. While these species share the same 2n and karyotypes, their congeneric species of the H. malabaricus group show a notable chromosomal diversity in number, morphology, and sex chromosome systems. However, at the same time, significant changes were characterized at their inner chromosomal level, as well as in their genetic diversity, highlighting their current relationships resulting from different evolutionary histories. Full article
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
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17 pages, 2300 KiB  
Article
Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats
by Isidoro Feliciello, Antonio Sermek, Željka Pezer, Maja Matulić and Đurđica Ugarković
Genes 2020, 11(6), 663; https://doi.org/10.3390/genes11060663 - 18 Jun 2020
Cited by 11 | Viewed by 2938
Abstract
Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed [...] Read more.
Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of “silent” H3K9me3 and “active” H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1–2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes. Full article
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
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Review

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27 pages, 2496 KiB  
Review
The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes
by Dareen Almojil, Yann Bourgeois, Marcin Falis, Imtiyaz Hariyani, Justin Wilcox and Stéphane Boissinot
Genes 2021, 12(6), 918; https://doi.org/10.3390/genes12060918 - 15 Jun 2021
Cited by 27 | Viewed by 6590
Abstract
Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being [...] Read more.
Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered. Full article
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
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22 pages, 1449 KiB  
Review
Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution
by Jérémy Barbier, Cédric Vaillant, Jean-Nicolas Volff, Frédéric G. Brunet and Benjamin Audit
Genes 2021, 12(6), 851; https://doi.org/10.3390/genes12060851 - 01 Jun 2021
Cited by 5 | Viewed by 3254
Abstract
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on [...] Read more.
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics. Full article
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
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26 pages, 1833 KiB  
Review
The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi
by Anton Gorkovskiy and Kevin J. Verstrepen
Genes 2021, 12(5), 699; https://doi.org/10.3390/genes12050699 - 08 May 2021
Cited by 12 | Viewed by 4597
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify [...] Read more.
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV. Full article
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
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