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Evolution, Composition and Regulation of Supernumerary B Chromosomes
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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) | Viewed by 85163

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Andreas Houben

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

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

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

E-Mail Website
Guest Editor
Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB SB RAS), 630090 Novosibirsk, Russia
Interests: evolution of vertebrate genomes; sex determination and sex chromosomes; B chromosomes; comparative genomics
Special Issues, Collections and Topics in MDPI journals

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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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

  • 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 (18 papers)

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Editorial

Jump to: Research, Review, Other

4 pages, 168 KiB  
Editorial
Evolution, Composition and Regulation of Supernumerary B Chromosomes
by Andreas Houben, Neil Jones, Cesar Martins and Vladimir Trifonov
Genes 2019, 10(2), 161; https://doi.org/10.3390/genes10020161 - 20 Feb 2019
Cited by 19 | Viewed by 3757
Abstract
Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi [...] Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)

Research

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20 pages, 3203 KiB  
Article
Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes
by Frances E. Clark, Matthew A. Conte and Thomas D. Kocher
Genes 2018, 9(12), 610; https://doi.org/10.3390/genes9120610 - 05 Dec 2018
Cited by 19 | Viewed by 3586
Abstract
B chromosomes (Bs) were discovered a century ago, and since then, most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many [...] Read more.
B chromosomes (Bs) were discovered a century ago, and since then, most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin, structure, function, and evolution of B chromosomes remain unanswered. Here, we identify B chromosome sequences from several species of cichlid fish from Lake Malawi by examining the ratios of DNA sequence coverage in individuals with or without B chromosomes. We examined the efficiency of this method, and compared results using both Illumina and PacBio sequence data. The B chromosome sequences detected in 13 individuals from 7 species were compared to assess the rates of sequence replacement. B-specific sequence common to at least 12 of the 13 datasets were identified as the “Core” B chromosome. The location of B sequence homologs throughout the genome provides further support for theories of B chromosome evolution. Finally, we identified genes and gene fragments located on the B chromosome, some of which may regulate the segregation and maintenance of the B chromosome. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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15 pages, 2518 KiB  
Article
Satellite DNAs Unveil Clues about the Ancestry and Composition of B Chromosomes in Three Grasshopper Species
by Diogo Milani, Vanessa B. Bardella, Ana B. S. M. Ferretti, Octavio M. Palacios-Gimenez, Adriana de S. Melo, Rita C. Moura, Vilma Loreto, Hojun Song and Diogo C. Cabral-de-Mello
Genes 2018, 9(11), 523; https://doi.org/10.3390/genes9110523 - 26 Oct 2018
Cited by 19 | Viewed by 3878
Abstract
Supernumerary (B) chromosomes are dispensable genomic elements occurring frequently among grasshoppers. Most B chromosomes are enriched with repetitive DNAs, including satellite DNAs (satDNAs) that could be implicated in their evolution. Although studied in some species, the specific ancestry of B chromosomes is difficult [...] Read more.
Supernumerary (B) chromosomes are dispensable genomic elements occurring frequently among grasshoppers. Most B chromosomes are enriched with repetitive DNAs, including satellite DNAs (satDNAs) that could be implicated in their evolution. Although studied in some species, the specific ancestry of B chromosomes is difficult to ascertain and it was determined in only a few examples. Here we used bioinformatics and cytogenetics to characterize the composition and putative ancestry of B chromosomes in three grasshopper species, Rhammatocerus brasiliensis, Schistocerca rubiginosa, and Xyleus discoideus angulatus. Using the RepeatExplorer pipeline we searched for the most abundant satDNAs in Illumina sequenced reads, and then we generated probes used in fluorescent in situ hybridization (FISH) to determine chromosomal position. We used this information to infer ancestry and the events that likely occurred at the origin of B chromosomes. We found twelve, nine, and eighteen satDNA families in the genomes of R. brasiliensis, S. rubiginosa, and X. d. angulatus, respectively. Some satDNAs revealed clustered organization on A and B chromosomes varying in number of sites and position along chromosomes. We did not find specific satDNA occurring in the B chromosome. The satDNAs shared among A and B chromosomes support the idea of putative intraspecific ancestry from small autosomes in the three species, i.e., pair S11 in R. brasiliensis, pair S9 in S. rubiginosa, and pair S10 in X. d. angulatus. The possibility of involvement of other chromosomal pairs in B chromosome origin is also hypothesized. Finally, we discussed particular aspects in composition, origin, and evolution of the B chromosome for each species. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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19 pages, 3065 KiB  
Article
B Chromosomes in Grasshoppers: Different Origins and Pathways to the Modern Bs
by Ilyas Yerkinovich Jetybayev, Alexander Gennadievich Bugrov, Victoria Vladimirovna Dzuybenko and Nikolay Borisovich Rubtsov
Genes 2018, 9(10), 509; https://doi.org/10.3390/genes9100509 - 18 Oct 2018
Cited by 11 | Viewed by 4220
Abstract
B chromosomes (Bs) were described in most taxa of eukaryotes and in around 11.9% of studied Orthopteran species. In some grasshopper species, their evolution has led to many B chromosome morphotypes. We studied the Bs in nine species (Nocaracris [...] Read more.
B chromosomes (Bs) were described in most taxa of eukaryotes and in around 11.9% of studied Orthopteran species. In some grasshopper species, their evolution has led to many B chromosome morphotypes. We studied the Bs in nine species (Nocaracris tardus, Nocaracris cyanipes, Aeropus sibiricus, Chorthippus jacobsoni, Chorthippus apricarius, Bryodema gebleri, Asiotmethis heptapotamicus songoricus, Podisma sapporensis, and Eyprepocnemis plorans), analyzing their possible origin and further development. The studied Bs consisted of C-positive or C-positive and C-negative regions. Analyzing new data and considering current hypotheses, we suggest that Bs in grasshoppers could arise through different mechanisms and from different chromosomes of the main set. We gave our special attention to the Bs with C-negative regions and suggest a new hypothesis of B chromosome formation from large or medium autosomes. This hypothesis includes dissemination of repetitive sequences and development of intercalary heterochromatic blocks in euchromatic chromosome arm followed by deletion of euchromatic regions located between them. The hypothesis is based on the findings of the Eyprepocnemis plorans specimens with autosome containing numerous intercalary repeat clusters, analysis of C-positive Bs in Eyprepocnemis plorans and Podisma sapporensis containing intercalary and terminal C-negative regions, and development of heterochromatic neo-Y chromosome in some Pamphagidae grasshoppers. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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11 pages, 1843 KiB  
Article
B Chromosome System in the Korean Field Mouse Apodemus peninsulae Thomas 1907 (Rodentia, Muridae)
by Yuri M. Borisov and Igor A. Zhigarev
Genes 2018, 9(10), 472; https://doi.org/10.3390/genes9100472 - 27 Sep 2018
Cited by 12 | Viewed by 3589
Abstract
In this paper, we analyzed B chromosome variation in Korean field mouse Apodemus peninsulae Thomas 1907 (Rodentia, Muridae) based on a 40-year study of karyotypes collected from geographically distant populations in East Siberia, North Mongolia, China, the Russian Far East, and Japan (Hokkaido). [...] Read more.
In this paper, we analyzed B chromosome variation in Korean field mouse Apodemus peninsulae Thomas 1907 (Rodentia, Muridae) based on a 40-year study of karyotypes collected from geographically distant populations in East Siberia, North Mongolia, China, the Russian Far East, and Japan (Hokkaido). We developed the database of individual variants of B chromosome systems in A. peninsulae. In Siberian populations all animals had Bs. The karyotypes of the studied animals contain from 1 to 30 Вs differing in size and morphology. Analysis of B chromosome systems in 598 individuals from different localities of the range shows the presence of 286 variants of Вs combinations in these animals. Unique sets of B morphotypes make up most of these variants (64.7 ± 1.3%), probably suggesting that individual Bs systems normally result from stochastic processes in the populations. The proportion of animals with a large number of Bs gradually decreases, probably due to increased complexities in the inheritance of large numbers of Bs. A. peninsulae is thus proposed as a good model for studying the origin and evolution of extra elements in the karyotype. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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10 pages, 3743 KiB  
Article
Euchromatic Supernumerary Chromosomal Segments—Remnants of Ongoing Karyotype Restructuring in the Prospero autumnale Complex?
by Tae-Soo Jang, John S. Parker and Hanna Weiss-Schneeweiss
Genes 2018, 9(10), 468; https://doi.org/10.3390/genes9100468 - 27 Sep 2018
Cited by 6 | Viewed by 3661
Abstract
Supernumerary chromosomal segments (SCSs) represent additional chromosomal material that, unlike B chromosomes, is attached to the standard chromosome complement. The Prospero autumnale complex (Hyacinthaceae) is polymorphic for euchromatic large terminal SCSs located on the short arm of chromosome 1 in diploid cytotypes AA [...] Read more.
Supernumerary chromosomal segments (SCSs) represent additional chromosomal material that, unlike B chromosomes, is attached to the standard chromosome complement. The Prospero autumnale complex (Hyacinthaceae) is polymorphic for euchromatic large terminal SCSs located on the short arm of chromosome 1 in diploid cytotypes AA and B7B7, and tetraploid AAB7B7 and B6B6B7B7, in addition to on the short arm of chromosome 4 in polyploid B7B7B7B7 and B7B7B7B7B7B7 cytotypes. The genomic composition and evolutionary relationships among these SCSs have been assessed using fluorescence in situ hybridisation (FISH) with 5S and 35S ribosomal DNAs (rDNAs), satellite DNA PaB6, and a vertebrate-type telomeric repeat TTAGGG. Neither of the rDNA repeats were detected in SCSs, but most contained PaB6 and telomeric repeats, although these never spanned whole SCSs. Genomic in situ hybridisation (GISH) using A, B6, and B7 diploid genomic parental DNAs as probes revealed the consistently higher genomic affinity of SCSs in diploid hybrid B6B7 and allopolyploids AAB7B7 and B6B6B7B7 to genomic DNA of the B7 diploid cytotype. GISH results suggest a possible early origin of SCSs, especially that on chromosome 1, as by-products of the extensive genome restructuring within a putative ancestral P. autumnale B7 genome, predating the complex diversification at the diploid level and perhaps linked to B-chromosome evolution. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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15 pages, 2182 KiB  
Article
B Chromosomes of the Asian Seabass (Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations
by Aleksey Komissarov, Shubha Vij, Andrey Yurchenko, Vladimir Trifonov, Natascha Thevasagayam, Jolly Saju, Prakki Sai Rama Sridatta, Kathiresan Purushothaman, Alexander Graphodatsky, László Orbán and Inna Kuznetsova
Genes 2018, 9(10), 464; https://doi.org/10.3390/genes9100464 - 20 Sep 2018
Cited by 11 | Viewed by 4288
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- [...] Read more.
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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14 pages, 812 KiB  
Article
Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes
by Alexey I. Makunin, Svetlana A. Romanenko, Violetta R. Beklemisheva, Polina L. Perelman, Anna S. Druzhkova, Kristina O. Petrova, Dmitry Yu. Prokopov, Ekaterina N. Chernyaeva, Jennifer L. Johnson, Anna V. Kukekova, Fengtang Yang, Malcolm A. Ferguson-Smith, Alexander S. Graphodatsky and Vladimir A. Trifonov
Genes 2018, 9(8), 405; https://doi.org/10.3390/genes9080405 - 10 Aug 2018
Cited by 22 | Viewed by 5314
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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18 pages, 3956 KiB  
Article
Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata
by Rafael L. B. Coan and Cesar Martins
Genes 2018, 9(6), 269; https://doi.org/10.3390/genes9060269 - 23 May 2018
Cited by 29 | Viewed by 6224
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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17 pages, 586 KiB  
Review
Origin, Behaviour, and Transmission of B Chromosome with Special Reference to Plantago lagopus
by Manoj K. Dhar, Jasmeet Kour and Sanjana Kaul
Genes 2019, 10(2), 152; https://doi.org/10.3390/genes10020152 - 18 Feb 2019
Cited by 15 | Viewed by 4790
Abstract
B chromosomes have been reported in many eukaryotic organisms. These chromosomes occur in addition to the standard complement of a species. Bs do not pair with any of the A chromosomes and they have generally been considered to be non-essential and genetically inert. [...] Read more.
B chromosomes have been reported in many eukaryotic organisms. These chromosomes occur in addition to the standard complement of a species. Bs do not pair with any of the A chromosomes and they have generally been considered to be non-essential and genetically inert. However, due to tremendous advancements in the technologies, the molecular composition of B chromosomes has been determined. The sequencing data has revealed that B chromosomes have originated from A chromosomes and they are rich in repetitive elements. In our laboratory, a novel B chromosome was discovered in Plantago lagopus. Using molecular cytogenetic techniques, the B chromosome was found to be composed of ribosomal DNA sequences. However, further characterization of the chromosome using next generation sequencing (NGS) etc. revealed that the B chromosome is a mosaic of sequences derived from A chromosomes, 5S ribosomal DNA (rDNA), 45S rDNA, and various types of repetitive elements. The transmission of B chromosome through the female sex track did not follow the Mendelian principles. The chromosome was found to have drive due to which it was perpetuating in populations. The present paper attempts to summarize the information on nature, transmission, and origin of B chromosomes, particularly the current status of our knowledge in P. lagopus. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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15 pages, 1244 KiB  
Review
Evolution of Plant B Chromosome Enriched Sequences
by André Marques, Sonja Klemme and Andreas Houben
Genes 2018, 9(10), 515; https://doi.org/10.3390/genes9100515 - 22 Oct 2018
Cited by 24 | Viewed by 7749 | Correction
Abstract
B chromosomes are supernumerary chromosomes found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several distinct types of repeated DNA elements. Although the evolution of B chromosomes has been the subject of numerous studies, the [...] Read more.
B chromosomes are supernumerary chromosomes found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several distinct types of repeated DNA elements. Although the evolution of B chromosomes has been the subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences are not fully understood. Recently, new genomic approaches have shed light on the origin and accumulation of different classes of repetitive sequences in the process of B chromosome formation and evolution. Here we discuss the impact of repetitive sequences accumulation on the evolution of plant B chromosomes. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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19 pages, 1418 KiB  
Review
Sequence Composition and Evolution of Mammalian B Chromosomes
by Nikolay B. Rubtsov and Yury M. Borisov
Genes 2018, 9(10), 490; https://doi.org/10.3390/genes9100490 - 10 Oct 2018
Cited by 17 | Viewed by 6055
Abstract
B chromosomes (Bs) revealed more than a hundred years ago remain to be some of the most mysterious elements of the eukaryotic genome. Their origin and evolution, DNA composition, transcriptional activity, impact on adaptiveness, behavior in meiosis, and transfer to the next generation [...] Read more.
B chromosomes (Bs) revealed more than a hundred years ago remain to be some of the most mysterious elements of the eukaryotic genome. Their origin and evolution, DNA composition, transcriptional activity, impact on adaptiveness, behavior in meiosis, and transfer to the next generation require intensive investigations using modern methods. Over the past years, new experimental techniques have been applied and helped us gain a deeper insight into the nature of Bs. Here, we consider mammalian Bs, taking into account data on their DNA sequencing, transcriptional activity, positions in nuclei of somatic and meiotic cells, and impact on genome functioning. Comparative cytogenetics of Bs suggests the existence of different mechanisms of their formation and evolution. Due to the long and complicated evolvement of Bs, the similarity of their morphology could be explained by the similar mechanisms involved in their development while the difference between Bs even of the same origin could appear due to their positioning at different stages of their evolution. A complex analysis of their DNA composition and other features is required to clarify the origin and evolutionary history of Bs in the species studied. The intraspecific diversity of Bs makes this analysis a very important element of B chromosome studies. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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27 pages, 353 KiB  
Review
B Chromosomes in Populations of Mammals Revisited
by Mladen Vujošević, Marija Rajičić and Jelena Blagojević
Genes 2018, 9(10), 487; https://doi.org/10.3390/genes9100487 - 09 Oct 2018
Cited by 29 | Viewed by 3904
Abstract
The study of B chromosomes (Bs) started more than a century ago, while their presence in mammals dates since 1965. As the past two decades have seen huge progress in application of molecular techniques, we decided to throw a glance on new data [...] Read more.
The study of B chromosomes (Bs) started more than a century ago, while their presence in mammals dates since 1965. As the past two decades have seen huge progress in application of molecular techniques, we decided to throw a glance on new data on Bs in mammals and to review them. We listed 85 mammals with Bs that make 1.94% of karyotypically studied species. Contrary to general view, a typical B chromosome in mammals appears both as sub- or metacentric that is the same size as small chromosomes of standard complement. Both karyotypically stable and unstable species possess Bs. The presence of Bs in certain species influences the cell division, the degree of recombination, the development, a number of quantitative characteristics, the host-parasite interactions and their behaviour. There is at least some data on molecular structure of Bs recorded in nearly a quarter of species. Nevertheless, a more detailed molecular composition of Bs presently known for six mammalian species, confirms the presence of protein coding genes, and the transcriptional activity for some of them. Therefore, the idea that Bs are inert is outdated, but the role of Bs is yet to be determined. The maintenance of Bs is obviously not the same for all species, so the current models must be adapted while bearing in mind that Bs are not inactive as it was once thought. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
10 pages, 907 KiB  
Review
The Behavior of the Maize B Chromosome and Centromere
by Handong Su, Yalin Liu, Yang Liu, James A. Birchler and Fangpu Han
Genes 2018, 9(10), 476; https://doi.org/10.3390/genes9100476 - 01 Oct 2018
Cited by 7 | Viewed by 4872
Abstract
The maize B chromosome is a non-essential chromosome with an accumulation mechanism. The dispensable nature of the B chromosome facilitates many types of genetic studies in maize. Maize lines with B chromosomes have been widely used in studies of centromere functions. Here, we [...] Read more.
The maize B chromosome is a non-essential chromosome with an accumulation mechanism. The dispensable nature of the B chromosome facilitates many types of genetic studies in maize. Maize lines with B chromosomes have been widely used in studies of centromere functions. Here, we discuss the maize B chromosome alongside the latest progress of B centromere activities, including centromere misdivision, inactivation, reactivation, and de novo centromere formation. The meiotic features of the B centromere, related to mini-chromosomes and the control of the size of the maize centromere, are also discussed. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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8 pages, 761 KiB  
Review
B Chromosomes in the Drosophila Genus
by Stacey L. Hanlon and R. Scott Hawley
Genes 2018, 9(10), 470; https://doi.org/10.3390/genes9100470 - 27 Sep 2018
Cited by 4 | Viewed by 5655
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 use of next-generation sequencing for B chromosome genomic analysis. Within the genus Drosophila, [...] Read more.
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 use 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 a single laboratory stock of Drosophila melanogaster. In this paper, we review the B chromosomes that have been identified within the Drosophila genus and pay special attention to those recently found in D. melanogaster. These newly-discovered B chromosomes have centromeres, telomeres, and a number of simple satellite repeats. They also appear to be entirely heterochromatic since next-generation sequencing of isolated B chromosomes did not detect sequences associated with known genic regions. We also summarize what effects the B chromosomes have been found to have on the A chromosomes. Lastly, we highlight some of the outstanding questions regarding B chromosome biology and discuss how studying B chromosomes in Drosophila melanogaster, which is a versatile model system with a wealth of genetic and genomic tools, may advance our understanding of the B chromosome’s unique biology. Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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9 pages, 13300 KiB  
Review
L Chromosome Behaviour and Chromosomal Imprinting in Sciara Coprophila
by Prim B. Singh and Stepan N. Belyakin
Genes 2018, 9(9), 440; https://doi.org/10.3390/genes9090440 - 03 Sep 2018
Cited by 7 | Viewed by 4945
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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9 pages, 844 KiB  
Review
Transmission and Drive Involving Parasitic B Chromosomes
by R.N. Jones
Genes 2018, 9(8), 388; https://doi.org/10.3390/genes9080388 - 31 Jul 2018
Cited by 26 | Viewed by 4147
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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1 pages, 168 KiB  
Correction
Correction: Marques, A. et al. Evolution of Plant B Chromosome Enriched Sequences. Genes 2018, 9, 515
by André Marques, Sonja Klemme and Andreas Houben
Genes 2019, 10(2), 85; https://doi.org/10.3390/genes10020085 - 26 Jan 2019
Cited by 8 | Viewed by 2037
Abstract
The authors wish to make the following modification in their review [...] Full article
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
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