Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.1
3.5
Journals
Genes
Special Issues
Structural Genetic Variation
share announcement

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: closed (1 October 2021) | Viewed by 4569

Special Issue Editors

Dr. José M. Ranz

E-Mail 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, Collections and Topics in MDPI journals
Dr. J.J. Emerson

E-Mail 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 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

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

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

14 pages, 2376 KiB  
Article
The Formation of Neochromosomes during Experimental Evolution in the Yeast Saccharomyces cerevisiae
by Agnès Thierry, Varun Khanna and Bernard Dujon
Genes 2021, 12(11), 1678; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111678 - 23 Oct 2021
Viewed by 1557
Abstract
Novel, large-scale structural mutations were previously discovered during the cultivation of engineered Saccharomyces cerevisiae strains in which essential tRNA synthetase genes were replaced by their orthologs from the distantly related yeast Yarrowia lipolytica. Among those were internal segmental amplifications forming giant chromosomes [...] Read more.
Novel, large-scale structural mutations were previously discovered during the cultivation of engineered Saccharomyces cerevisiae strains in which essential tRNA synthetase genes were replaced by their orthologs from the distantly related yeast Yarrowia lipolytica. Among those were internal segmental amplifications forming giant chromosomes as well as complex segmental rearrangements associated with massive amplifications at an unselected short locus. The formation of such novel structures, whose stability is high enough to propagate over multiple generations, involved short repeated sequences dispersed in the genome (as expected), but also novel junctions between unrelated sequences likely triggered by accidental template switching within replication forks. Using the same evolutionary protocol, we now describe yet another type of major structural mutation in the yeast genome, the formation of neochromosomes, with functional centromeres and telomeres, made of extra copies of very long chromosomal segments ligated together in novel arrangements. The novel junctions occurred between short repeated sequences dispersed in the genome. They first resulted in the formation of an instable neochromosome present in a single copy in the diploid cells, followed by its replacement by a shorter, partially palindromic neochromosome present in two copies, whose stability eventually increased the chromosome number of the diploid strains harboring it. Full article
(This article belongs to the Special Issue Structural Genetic Variation)
►▼ Show Figures

Figure 1

11 pages, 4580 KiB  
Article
Compound Heterozygote of Point Mutation and Chromosomal Microdeletion Involving OTUD6B Coinciding with ZMIZ1 Variant in Syndromic Intellectual Disability
by Tim Phetthong, Arthaporn Khongkrapan, Natini Jinawath, Go-Hun Seo and Duangrurdee Wattanasirichaigoon
Genes 2021, 12(10), 1583; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101583 - 07 Oct 2021
Cited by 5 | Viewed by 2450
Abstract
The OTUD6B and ZMIZ1 genes were recently identified as causes of syndromic intellectual disability (ID) with shared phenotypes of facial dysmorphism, distal limb anomalies, and seizure disorders. OTUD6B- and ZMIZ1-related ID are inherited in autosomal recessive and autosomal dominant patterns, respectively. We report [...] Read more.
The OTUD6B and ZMIZ1 genes were recently identified as causes of syndromic intellectual disability (ID) with shared phenotypes of facial dysmorphism, distal limb anomalies, and seizure disorders. OTUD6B- and ZMIZ1-related ID are inherited in autosomal recessive and autosomal dominant patterns, respectively. We report a 5-year-old girl with developmental delay, facial phenotypes resembling Williams syndrome, and cardiac defects. The patient also had terminal broadening of the fingers and polydactyly. Cytogenomic microarray (CMA), whole exome sequencing (WES), and mRNA analysis were performed. The CMA showed a paternally inherited 0.118 Mb deletion of 8q21.3, chr8:92084087–92202189, with OTUD6B involved. The WES identified a hemizygous OTUD6B variant, c.873delA (p.Lys291AsnfsTer3). The mother was heterozygous for this allele. The WES also demonstrated a heterozygous ZMIZ1 variant, c.1491 + 2T > C, in the patient and her father. This ZMIZ1 variant yielded exon 14 skipping, as evidenced by mRNA study. We suggest that Williams syndrome-like phenotypes, namely, periorbital edema, hanging cheek, and long and smooth philtrum represent expanded phenotypes of OTUD6B-related ID. Our data expand the genotypic spectrum of OTUD6B- and ZMIZ1-related disorders. This is the first reported case of a compound heterozygote featuring point mutation, chromosomal microdeletion of OTUD6B, and the unique event of OTUD6B, coupled with ZMIZ1 variants. Full article
(This article belongs to the Special Issue Structural Genetic Variation)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop