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Editorial

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4 pages, 168 KiB

Open AccessEditorial

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 21 | Viewed by 4363

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

Open AccessArticle

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 - 5 Dec 2018

Cited by 20 | Viewed by 4125

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

Open AccessArticle

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 22 | Viewed by 4537

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

Open AccessArticle

B Chromosomes in Grasshoppers: Different Origins and Pathways to the Modern B_s

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 12 | Viewed by 4952

Abstract

B chromosomes (B_s) 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 B_s in nine species (Nocaracris [...] Read more.

B chromosomes (B_s) 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 B_s 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 B_s consisted of C-positive or C-positive and C-negative regions. Analyzing new data and considering current hypotheses, we suggest that B_s in grasshoppers could arise through different mechanisms and from different chromosomes of the main set. We gave our special attention to the B_s 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 B_s 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

Open AccessArticle

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 16 | Viewed by 4215

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

Open AccessArticle

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 4171

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

Open AccessArticle

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 13 | Viewed by 4936

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

Open AccessArticle

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 23 | Viewed by 6080

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

Open AccessArticle

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 33 | Viewed by 7029

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

Open AccessReview

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 20 | Viewed by 5579

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

Open AccessReview

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 28 | Viewed by 8564 | 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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Graphical abstract

19 pages, 1418 KiB

Open AccessReview

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 20 | Viewed by 6938

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

Open AccessReview

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 - 9 Oct 2018

Cited by 36 | Viewed by 4636

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

Open AccessReview

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 - 1 Oct 2018

Cited by 9 | Viewed by 5575

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

Open AccessReview

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 6 | Viewed by 6599

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

Open AccessReview

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 - 3 Sep 2018

Cited by 7 | Viewed by 5651

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

Open AccessReview

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 31 | Viewed by 4716

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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Other

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1 pages, 168 KiB

Open AccessCorrection

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 2 | Viewed by 2366

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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