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New Advances in Compositional Genome Evolution
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New Advances in Compositional Genome Evolution

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: closed (31 May 2022) | Viewed by 9759

Special Issue Editor

Dr. Radka Symonova

E-Mail Website
Guest Editor
Department of Fish and Zooplankton Ecology, University of Hradec Kralove, 500 03 Hradec Králové, Czech Republic
Interests: genome evolution; GC-biology; fish chromosomes; rDNA genes

Special Issue Information

Dear Colleagues,

Nucleotide composition, i.e., not only the primary DNA sequence but also the proportion of AT versus GC, is a crucial factor driving important genomic features like gene density, DNA methylation, DNA mutations, DNA replication timing, chromatin structure, proportion and types of transposons, nucleosome formation potential, and many more. However, despite the still increasing number of sequenced genomes, it is still unclear why mammalian and avian genomes are AT/GC heterogeneous, whereas genomes of lower vertebrates are AT/GC homogenous.

In this Special Issue, we aim to integrate the latest results from prokaryotes and eukaryotes, plants and animals, unicellular and multicellular organisms, and above all vertebrates to assess the currently relevant viewpoints of the compositional genome evolution. Namely, we aim to analyse GC-related structural as well as functional traits regarding neutral evolutionary processes and potential roles of selection in genomes and their transposons.

Dr. Radka Symonova
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • AT/GC evolution in prokaryotes
  • AT/GC evolution in eukaryotes
  • AT/GC evolution of eukaryotic transposons (active, inactive, DNA transposons, retrotransposons)
  • Role of selection in GC biology
  • Levels of gene expression and GC content

Published Papers (4 papers)

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Research

Jump to: Review

14 pages, 3599 KiB  
Article
Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish
by Marta Vohnoutová, Anastázie Sedláková and Radka Symonová
Int. J. Mol. Sci. 2023, 24(17), 13167; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241713167 - 24 Aug 2023
Viewed by 644
Abstract
The organization of the genome nucleotide (AT/GC) composition in vertebrates remains poorly understood despite the numerous genome assemblies available. Particularly, the origin of the AT/GC heterogeneity in amniotes, in comparison to the homogeneity in anamniotes, is controversial. Recently, several exceptions to this dichotomy [...] Read more.
The organization of the genome nucleotide (AT/GC) composition in vertebrates remains poorly understood despite the numerous genome assemblies available. Particularly, the origin of the AT/GC heterogeneity in amniotes, in comparison to the homogeneity in anamniotes, is controversial. Recently, several exceptions to this dichotomy were confirmed in an ancient fish lineage with mammalian AT/GC heterogeneity. Hence, our current knowledge necessitates a reevaluation considering this fact and utilizing newly available data and tools. We analyzed fish genomes in silico with as low user input as possible to compare previous approaches to assessing genome composition. Our results revealed a disparity between previously used plots of GC% and histograms representing the authentic distribution of GC% values in genomes. Previous plots heavily reduced the range of GC% values in fish to comply with the alleged AT/GC homogeneity and AT-richness of their genomes. We illustrate how the selected sequence size influences the clustering of GC% values. Previous approaches that disregarded chromosome and genome sizes, which are about three times smaller in fish than in mammals, distorted their results and contributed to the persisting confusion about fish genome composition. Chromosome size and their transposons may drive the AT/GC heterogeneity apparent on mammalian chromosomes, whereas far less in fishes. Full article
(This article belongs to the Special Issue New Advances in Compositional Genome Evolution)
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9 pages, 2314 KiB  
Article
Slaying (Yet Again) the Brain-Eating Zombie Called the “Isochore Theory”: A Segmentation Algorithm Used to “Confirm” the Existence of Isochores Creates “Isochores” Where None Exist
by Dan Graur
Int. J. Mol. Sci. 2022, 23(12), 6558; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126558 - 12 Jun 2022
Cited by 2 | Viewed by 1284
Abstract
The isochore theory, which was proposed more than 40 years ago, depicts the mammalian genome as a mosaic of long, homogeneous regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five [...] Read more.
The isochore theory, which was proposed more than 40 years ago, depicts the mammalian genome as a mosaic of long, homogeneous regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five compositionally distinct isochore families. The isochore theory, in all its reincarnations, has been repeatedly falsified in the literature, yet isochore proponents have persistently resurrected it by either redefining isochores or by proposing alternative means of testing the theory. Here, I deal with the latest attempt to salvage this seemingly immortal zombie—a sequence segmentation method called isoSegmenter, which was claimed to “identify” isochores while at the same time disregarding the main characteristic attribute of isochores—compositional homogeneity. I used a series of controlled, randomly generated simulated sequences as a benchmark to study the performance of isoSegmenter. The main advantage of using simulated sequences is that, unlike real data, the exact start and stop point of any isochore or homogeneous compositional domain is known. Based on three key performance metrics—sensitivity, precision, and Jaccard similarity index—isoSegmenter was found to be vastly inferior to isoPlotter, a segmentation algorithm with no user input. Moreover, isoSegmenter identified isochores where none exist and failed to identify compositionally homogeneous sequences that were shorter than 100−200 kb. Will this zillionth refutation of “isochores” ensure a final and permanent entombment of the isochore theory? This author is not holding his breath. Full article
(This article belongs to the Special Issue New Advances in Compositional Genome Evolution)
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Review

Jump to: Research

20 pages, 665 KiB  
Review
Current Methods for Recombination Detection in Bacteria
by Anton E. Shikov, Yury V. Malovichko, Anton A. Nizhnikov and Kirill S. Antonets
Int. J. Mol. Sci. 2022, 23(11), 6257; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116257 - 02 Jun 2022
Cited by 11 | Viewed by 4554
Abstract
The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both [...] Read more.
The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of software. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic approaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed. Full article
(This article belongs to the Special Issue New Advances in Compositional Genome Evolution)
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13 pages, 579 KiB  
Review
On the Base Composition of Transposable Elements
by Stéphane Boissinot
Int. J. Mol. Sci. 2022, 23(9), 4755; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23094755 - 26 Apr 2022
Cited by 7 | Viewed by 2029
Abstract
Transposable elements exhibit a base composition that is often different from the genomic average and from hosts’ genes. The most common compositional bias is towards Adenosine and Thymine, although this bias is not universal, and elements with drastically different base composition can coexist [...] Read more.
Transposable elements exhibit a base composition that is often different from the genomic average and from hosts’ genes. The most common compositional bias is towards Adenosine and Thymine, although this bias is not universal, and elements with drastically different base composition can coexist within the same genome. The AT-richness of transposable elements is apparently maladaptive because it results in poor transcription and sub-optimal translation of proteins encoded by the elements. The cause(s) of this unusual base composition remain unclear and have yet to be investigated. Here, I review what is known about the nucleotide content of transposable elements and how this content can affect the genome of their host as well as their own replication. The compositional bias of transposable elements could result from several non-exclusive processes including horizontal transfer, mutational bias, and selection. It appears that mutation alone cannot explain the high AT-content of transposons and that selection plays a major role in the evolution of the compositional bias. The reason why selection would favor a maladaptive nucleotide content remains however unexplained and is an area of investigation that clearly deserves attention. Full article
(This article belongs to the Special Issue New Advances in Compositional Genome Evolution)
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