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: closed (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

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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 (5 papers)

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Research

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Open AccessArticle B Chromosomes of the Asian Seabass (Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations
Genes 2018, 9(10), 464; https://doi.org/10.3390/genes9100464
Received: 4 August 2018 / Revised: 6 September 2018 / Accepted: 12 September 2018 / Published: 20 September 2018
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Abstract
The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT-
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The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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Open AccessArticle Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes
Received: 6 July 2018 / Revised: 29 July 2018 / Accepted: 7 August 2018 / Published: 10 August 2018
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Abstract
B chromosomes (Bs) represent a variable addition to the main karyotype in some lineages of animals and plants. Bs accumulate through non-Mendelian inheritance and become widespread in populations. Despite the presence of multiple genes, most Bs lack specific phenotypic effects, although their influence
[...] Read more.
B chromosomes (Bs) represent a variable addition to the main karyotype in some lineages of animals and plants. Bs accumulate through non-Mendelian inheritance and become widespread in populations. Despite the presence of multiple genes, most Bs lack specific phenotypic effects, although their influence on host genome epigenetic status and gene expression are recorded. Previously, using sequencing of isolated Bs of ruminants and rodents, we demonstrated that Bs originate as segmental duplications of specific genomic regions, and subsequently experience pseudogenization and repeat accumulation. Here, we used a similar approach to characterize Bs of the red fox (Vulpes vulpes L.) and the Chinese raccoon dog (Nyctereutes procyonoides procyonoides Gray). We confirm the previous findings of the KIT gene on Bs of both species, but demostrate an independent origin of Bs in these species, with two reused regions. Comparison of gene ensembles in Bs of canids, ruminants, and rodents once again indicates enrichment with cell-cycle genes, development-related genes, and genes functioning in the neuron synapse. The presence of B-chromosomal copies of genes involved in cell-cycle regulation and tissue differentiation may indicate importance of these genes for B chromosome establishment. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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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
Cited by 1 | 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)
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Review

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Open AccessReview L Chromosome Behaviour and Chromosomal Imprinting in Sciara Coprophila
Received: 19 July 2018 / Revised: 29 August 2018 / Accepted: 29 August 2018 / Published: 3 September 2018
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Abstract
The retention of supernumerary chromosomes in the germ-line of Sciara coprophila is part of a highly-intricate pattern of chromosome behaviours that have fascinated cytogeneticists for over 80 years. Germ-line limited (termed L or “limited”) chromosomes are cytologically heterochromatic and late-replicating, with more recent
[...] Read more.
The retention of supernumerary chromosomes in the germ-line of Sciara coprophila is part of a highly-intricate pattern of chromosome behaviours that have fascinated cytogeneticists for over 80 years. Germ-line limited (termed L or “limited”) chromosomes are cytologically heterochromatic and late-replicating, with more recent studies confirming they possess epigenetic hallmarks characteristic of constitutive heterochromatin. Little is known about their genetic constitution although they have been found to undergo cycles of condensation and de-condensation at different stages of development. Unlike most supernumeraries, the L chromosomes in S. coprophila are thought to be indispensable, although in two closely related species Sciara ocellaris and Sciara reynoldsi the L chromosomes, have been lost during evolution. Here, we review what we know about L chromosomes in Sciara coprophila. We end by discussing how study of the L chromosome condensation cycle has provided insight into the site and timing of both the erasure of parental “imprints” and also the placement of a putative “imprint” that might be carried by the sperm into the egg. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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Open AccessReview Transmission and Drive Involving Parasitic B Chromosomes
Received: 25 June 2018 / Revised: 26 July 2018 / Accepted: 26 July 2018 / Published: 31 July 2018
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Abstract
B chromosomes (Bs) 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
[...] Read more.
B chromosomes (Bs) 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. It is also becoming increasingly clear that the host genomes are developing their own mechanisms to resist the impact of the harmful effects of the Bs. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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