Special Issue "Evolution, Composition and Regulation of Supernumerary B Chromosomes"

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: 31 August 2018

Special Issue Editors

Guest Editor
Prof. Andreas Houben

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben,Corrensstraße 3, 06466 Stadt Seeland, Germany
Website | E-Mail
Interests: chromosome structure; B chromosome; centromere; CENH3; genome evolution
Guest Editor
Prof. Neil Jones

Aberystwyth University, Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Penglais Campus, Aberystwyth SY23 3DA, UK
Website | E-Mail
Phone: 44 (0)1970 622230
Interests: Plant cytogenetics; B chromosomes; genome evolution
Guest Editor
Prof. Cesar Martins

Department of Morphology, Institute of Biosciences, UNESP - São Paulo State University, 18618-689, Botucatu, SP, Brazil
Website | E-Mail
Interests: B chromosomes; genome evolution; evolution; comparative genomics
Guest Editor
Dr. Vladimir Trifonov

Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB SB RAS), 630090 Novosibirsk, Russia
Website | E-Mail
Interests: evolution of vertebrate genomes; sex determination and sex chromosomes; B chromosomes; comparative genomics

Special Issue Information

Dear Colleagues,

Supernumerary B chromosomes are dispensable genetic elements found in thousands of species of plants and animals, and some fungi. Since their discovery, more than a century ago, they have been a source of puzzlement, as they only occur in some members of a population and are absent from others. When they do occur, they are often harmful, and in the absence of 'selfishness', based on mechanisms of mitotic and meiotic drive, there appears to be no obvious reasons for their existence. Cytogeneticists have long wrestled with questions about the biological existence of these enigmatic B chromosomes, including their lack of any adaptive properties, apparent absence of functional genes, their origin, sequence organization and co-evolution as nuclear parasites. Emerging new technologies are now enabling researchers to step up a gear, to look enthusiastically beyond the previous limits of the horizon, and to uncover the secrets of these 'silent' elements. Detailed investigations into their DNA composition, transcriptional activity and effects on the host transcriptome profile are beginning to uncover a wealth of new information. Contributing authors come from across a wide range of species, and different systems, and their thematic output will give a broad view and a significant step forward to understanding this perplexing biological story.

Prof. Andreas Houben
Prof. Neil Jones
Prof. Cesar Martins
Dr. Vladimir Trifonov
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 1600 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

  • accessory chromosome
  • B chromosome
  • supernumerary chromosome
  • selfish DNA
  • degeneration
  • chromosome drive
  • gene silencing
  • heterochromatization
  • Muller’s ratchet
  • mutation accumulation
  • pseudogenization
  • recombination
  • repetitive DNA
  • retrotransposons
  • pseudogene
  • evolution
  • karyotype
  • next generation sequencing
  • chromosome thripsis

Published Papers (1 paper)

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Research

Open AccessArticle Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata
Received: 17 March 2018 / Revised: 16 May 2018 / Accepted: 17 May 2018 / Published: 23 May 2018
PDF Full-text (3956 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a
[...] Read more.
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
Figures

Figure 1

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.

Tentative title: Transmission and drive involving parasitic B chromosomes

Author: Neil Jones

Affiliation: Aberystwyth University, Aberystwyth, UK

Tentative abstract: B chromosomes are enigmatic additional elements in the genomes of thousands of species of plants, animals and fungi. How do these non-essential, harmful and parasitic chromosomes maintain their presence in their hosts, making demands on all the essential functions of their host genomes? The answer seems to be that they have mechanisms of drive which enable them to enhance their transmission rates by various processes of non-Mendelian inheritance. These processes are reviewed and discussed.

 

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Tentative Title: B chromosomes in the Drosophila genus

Authors: Stacey L. Hanlon[1] and R. Scott Hawley[1,2]

Affiliations: [1] Stowers Institute for Medical Research, Kansas City, MO, USA, and [2] Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA

Abstract: Our current knowledge of B chromosome biology has been augmented by an increase in the number and diversity of species observed to carry B chromosomes as well as the accessibility of next-generation sequencing for B chromosome genomic analysis.  Within the genus Drosophila, B chromosomes have been observed in a handful of species, but recently they were discovered in an individual laboratory stock of D. melanogaster.  Here we review the B chromosomes within the Drosophila genus and pay special attention to those recently found in D. melanogaster.  These newly-discovered B chromosomes were separated from the A chromosomes and analyzed via next-generation sequencing.  Though these B chromosomes do not have euchromatic sequence, they are enriched for simple heterochromatic repeats and transposable elements.  The high copy number of B chromosomes in their endogenous stock indicate they are likely subject to a drive mechanism, a phenomenon observed in several other B chromosome systems.  We then highlight some of the outstanding questions in the B chromosome field and discuss how studying B chromosomes in this versatile model system with a wealth of genetic and genomic tools may advance our understanding of the B chromosome's unique biology.

 

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Tentative Title: Phylogenomics of Fusarium oxysporum accessory Chromosomes 

Authors: Fokkens, L. and Rep, M. 

Affiliation: Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands

 Abstract: Background: The genome of Fusarium oxysporum f. sp. lycopersici 4287m(Fol4287) consists of 11 core and 4 accessory chromosomes. One of these accessory chromosomes – chromosome 14- is undoubtedly a pathogenicity chromosome as it contains all known effector genes and horizontal transfer of this chromosome to a non-pathogenic isolate, turns it pathogenic. Previous analyses, based on a concatenated alignment of genes that have a copy on the core genome, the accessory genome and in 6 selected other fungi, suggested that Fol4287 obtained accessory chromosomes through horizontal transfer from an unknown fungus. Results: Here we used phylogenomics to investigate whether all accessory chromosomes have a similar evolutionary history. We inferred gene trees for all Fol4287 genes and compared tree topologies between core and accessory genes, and between genes that are located on different chromosomes. We find that gene duplication plays an important role – which is not surprising since many accessory chromosomes contain large-scale (>100 kb) duplications. Moreover, we find that gene tree topology for about a quarter of accessory genes corresponds to the species tree, suggesting that these genes have moved from the core genome to the accessory genome. The other accessory genes have a patchy distribution in other fungi, but the topologies of their gene trees suggest that this is due to independent gene loss events in other fungi rather than horizontal transfer.

 

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Tentative Title: Sequencing of B chromosomes in red fox (Vulpes vulpes) and Chinese raccoon dog (Nyctereutes procyonoides procyonoides)

Author: Alexey Makunin

Affiliation: Institute Of Molecular And Cellular Biology SB RAS, Novosibirsk, Russia

Tentative Abstract: B chromosomes (Bs) represent the variable addition to the main karyotype in selected lineages of animals and plants. In contrast to other types of supernumerary chromosomes, Bs are found in a significant proportion of populations and often demonstrate non-mendelian inheritance resulting in accumulation through generations. Despite the presence of multiple genes, most B chromosomes lack specific phenotypic effects, although epigenetic and gene expression changes were recorded. Previously, using sequencing of isolated B chromosomes of ruminants and rodents, we demonstrated that Bs originate as segmental duplications of several genomic regions and subsequently experience pseudogenization and repeat accumulation. Here, we use a similar approach to characterize B chromosomes of red fox and Chinese raccoon dog. We confirm previous findings of several genes on B chromosomes, most notably protooncogenes KIT (in both species) and RET (in Chinese raccoon dog), and also characterize Bs’ repetitive DNA content and sequence variation. Our data point to independent origin of B chromosomes in these species, but with several shared regions. Comparison of gene ensembles in Bs of canids, ruminants, and rodents once again indicates an enrichment with cell-cycle-related functions, which suggests an important role of B-chromosomal gene copies in B chromosome establishment. 

 

 

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