Special Issue "Structural Genetic Variation"

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

Deadline for manuscript submissions: 1 April 2021.

Special Issue Editors

Dr. José M. Ranz
Website
Guest Editor
Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
Interests: functional and comparative genomics; evolution of the expression network; speciation
Special Issues and Collections in MDPI journals
Dr. J.J. Emerson
Website
Guest Editor
Department of Ecology and Evolutionary Biology, Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697 USA.
Interests: natural genetic variation; evolution; new genes; sex chromosome evolution; genetic architecture of gene expression variation

Special Issue Information

Dear Colleagues,

Large-scale changes in chromosomes not only remodel their structure but also can modify gene content, gene order, gene regulation, and can even create the raw material for new gene functions. In this way, structural variants are increasingly recognized as a category of genetic change, with high potential to impact the phenotype and organismal fitness, thus contributing to disease, adaptation, and species differentiation. Nevertheless, structural variation has been understudied, largely because technical limitations have prevented its reliable characterization at the sequence level, in turn hindering the proper analysis of the functional and phenotypic consequences of this variation.

In this Special Issue, we aim to publish review and original research papers that address a wide variety of topics associated with structural variation, including how to accurately discover and characterize structural variation using third-generation sequencing technologies, the quantification of the effects of structural variation on fitness, the characterization of the variation in repeats and selfish genetic elements, and how structural changes influence repertoires of gene function.

Dr. José M. Ranz
Dr. J.J. Emerson
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

  • Genome evolution
  • Structural variation
  • Reference-quality genome assemblies
  • Gene novelty
  • Adaptation
  • Phenotypic effects
  • Repeats

Published Papers

This special issue is now open for submission, see below for planned papers.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: The formation of neochromosomes during experimental evolution in the yeast Saccharomyces cerevisiae
Authors: Agnès Thierry; Varun Khanna; Bernard Dujon
Affiliation: Institut Pasteur, Department Genome and Genetics, 25 rue du Docteur Roux, F75724 Paris-CEDEX15, France
Abstract: Novel, large-scale structural mutations were previously discovered during cultivation of engineered Saccharomyces cerevisiae strains in which essential tRNA synthetase genes were replaced by their orthologs from Yarrowia lipolytica. Among those were giant chromosomes (macrotene) in which long internal chromosomal segments are multiply amplified in direct or inverted tandem orientation (1) or a shorter locus is massively amplified in association with multiple reassociations of long chromosomal segments at specific breakpoints (2). The structural mutants formed are stable enough to propagate in subsequent generations. Sequence analysis suggests accidental template switching within replication forks, likely due to interference between neighboring replicons, as the initiating mechanism of structural mutations whose final forms depend on the possibility of subsequent exchanges between short repeated sequences dispersed in genomes. Using the same evolutionary protocol, we now describe yet another type of major structural mutations, the formation of neochromosomes with functional centromeres and telomeres by the reassociation of copies of large segments from the different natural chromosomes of yeast. The molecular mechanisms at the origin of these mutations and those deduced from previous structures are discussed in relationship with the evolution of eukaryotic chromosomes. (1) Thierry, A. et al., (2015) Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes. Nature Communication 6:6154. (2) Thierry, A. et al., (2016) Massive amplification at an unselected locus accompanies complex chromosomal rearrangements in yeast. G3 6: 1201-1215.

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