Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds

AbstractHere, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (−B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.

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Plantago lagopus B Chromosome Is Enriched in 5S rDNA-Derived Satellite DNA

Cytogenetic and Genome Research ◽

10.1159/000444873 ◽

2016 ◽

Vol 148 (1) ◽

pp. 68-73 ◽

Cited By ~ 15

Author(s):

Katrin Kumke ◽

Jiří Macas ◽

Jörg Fuchs ◽

Lothar Altschmied ◽

Jasmeet Kour ◽

...

Keyword(s):

Repetitive Sequences ◽

Nuclear Genome ◽

5S Rdna ◽

B Chromosome ◽

B Chromosomes ◽

Specific Marker ◽

Sequencing Technology ◽

Plantago Lagopus ◽

Copy Dna ◽

Chromosome Segments

B chromosomes are supernumerary dispensable parts of the karyotype which appear in some individuals of some populations in some species. Using advanced sequencing technology, we in silico characterized the high-copy DNA composition of Plantago lagopus with and without B chromosomes. The nuclear genome (2.46 pg/2C) was found to be relatively rich in repetitive sequences, with highly and moderately repeated elements making up 68% of the genome. Besides a centromere-specific marker, we identified a B-specific satellite and a repeat enriched in polymorphic A chromosome segments. The B-specific tandem repeat PLsatB originated from sequence amplification including 5S rDNA fragments.

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Evolution of Plant B Chromosome Enriched Sequences

Genes ◽

10.3390/genes9100515 ◽

2018 ◽

Vol 9 (10) ◽

pp. 515 ◽

Cited By ~ 10

Author(s):

André Marques ◽

Sonja Klemme ◽

Andreas Houben

Keyword(s):

Repetitive Sequences ◽

B Chromosome ◽

B Chromosomes ◽

Dna Elements ◽

Formation And Evolution ◽

The Subject ◽

Chromosome Formation ◽

The Impact ◽

Normal Standard ◽

Shed Light

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.

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B Chromosomes in the Drosophila Genus

Genes ◽

10.3390/genes9100470 ◽

2018 ◽

Vol 9 (10) ◽

pp. 470 ◽

Cited By ~ 3

Author(s):

Stacey Hanlon ◽

R. Hawley

Keyword(s):

Drosophila Melanogaster ◽

Next Generation Sequencing ◽

Current Knowledge ◽

Genomic Analysis ◽

B Chromosome ◽

B Chromosomes ◽

Next Generation ◽

Satellite Repeats ◽

Genomic Tools ◽

Generation Sequencing

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.

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B Chromosome Diversity and Repetitive Sequence Distribution in an Isolated Population of Akodon montensis (Rodentia, Sigmodontinae)

Cytogenetic and Genome Research ◽

10.1159/000487471 ◽

2018 ◽

Vol 154 (2) ◽

pp. 79-85

Author(s):

Amanda A. Soares ◽

Jonathan P. Castro ◽

Pedro Balieiro ◽

Sidnei Dornelles ◽

Tiago M. Degrandi ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Repetitive Sequences ◽

5S Rdna ◽

B Chromosome ◽

B Chromosomes ◽

Telomeric Sequences ◽

Supernumerary Chromosomes ◽

Dna Libraries ◽

Eukaryotic Species ◽

Size And Morphology

B chromosomes are supernumerary chromosomes found in the karyotypes of approximately 15% of all eukaryotic species. They present parasitic behavior and do not follow the standard Mendelian pattern of inheritance, resulting in an imbalance in gametogenesis. The evolutionary dynamics of B chromosomes is still unknown for many species, but studies indicate that the accumulation of repetitive sequences plays an important role in the differentiation of these elements. We analyzed morphology, frequency, and possible homologies amongst different B chromosomes found in an isolated Akodon montensis population in southern Brazil. Repetitive sequences (18S, 5S rDNA and telomeric sequences) were used to test for their accumulation on the supernumerary chromosomes and describe their localization in the species. The results indicate 4 different B chromosome morphotypes, and DNA libraries were generated for 3 of them. 18S rDNA was labelled polymorphically, except in the B chromosomes, whereas the 5S rDNA was located exclusively in an interstitial position on the long arm of chromosome 5. Chromosome painting with the B probes based on FISH revealed a homologous composition for all B chromosome morphotypes and no homology with the chromosomes in the A complement. B chromosomes found in this population may have a common origin and subsequently diversified in size and morphology.

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Structural and Functional Analysis of Transposable Elements Focusing on B Chromosomes of the Cichlid Fish Astatotilapia latifasciata

10.20944/preprints201803.0145.v1 ◽

2018 ◽

Author(s):

Rafael Coan ◽

Cesar Martins

Keyword(s):

Transposable Elements ◽

Repetitive Sequences ◽

Chromosome Complement ◽

Cichlid Fish ◽

B Chromosome ◽

B Chromosomes ◽

Sequencing Data ◽

Taxonomic Groups ◽

African Cichlids

B chromosomes (B) 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). Bs origin is generally linked to the A chromosome complement (A). The first report of a B chromosome in African cichlids was on Astatotilapia latifasciata, which can harbor 0, 1 or 2 B chromosomes. Classical cytogenetics studies found high TE content on the species B chromosome. In this study, we aim to understand TE composition and expression on A. latifasciata genome and its relation to the B chromosome. We use bioinformatics analysis to explore TEs genome organization and also their composition on the B chromosome. Bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to 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 brain, muscle and male/female gonads. The evaluation of TE expression between B- and B+ individuals showed that few elements have differential expression among groups and expanded B elements were not highly transcribed. Putative silencing mechanisms may the acting on the B chromosome of A. latifasciata to prevent adverse consequences of repeat transcription and mobilization in the genome.

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Evolution of Plant B Chromosome Enriched Sequences

10.20944/preprints201809.0470.v1 ◽

2018 ◽

Author(s):

André Marques ◽

Sonja Klemme ◽

Andreas Houben

Keyword(s):

Repetitive Sequences ◽

B Chromosome ◽

B Chromosomes ◽

Supernumerary Chromosomes ◽

Formation And Evolution ◽

Chromosome Formation ◽

The Impact ◽

Normal Standard ◽

Shed Light

B chromosomes are supernumerary chromosomes which are found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several types of repeats. Although the evolution of B chromosomes has been subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences is 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.

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

Genes ◽

10.3390/genes9100509 ◽

2018 ◽

Vol 9 (10) ◽

pp. 509 ◽

Cited By ~ 8

Author(s):

Ilyas Jetybayev ◽

Alexander Bugrov ◽

Victoria Dzuybenko ◽

Nikolay Rubtsov

Keyword(s):

Repetitive Sequences ◽

B Chromosome ◽

B Chromosomes ◽

Eyprepocnemis Plorans ◽

Grasshopper Species ◽

Chromosome Formation ◽

Different Origins ◽

Further Development ◽

New Hypothesis ◽

Orthopteran Species

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.

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Spatial organization of fibroblast and spermatocyte nuclei with different B-chromosome content in Korean field mouse, Apodemus peninsulae (Rodentia, Muridae)

Genome ◽

10.1139/gen-2017-0029 ◽

2017 ◽

Vol 60 (10) ◽

pp. 815-824 ◽

Cited By ~ 4

Author(s):

Tatyana V. Karamysheva ◽

Anna A. Torgasheva ◽

Yaroslav R. Yefremov ◽

Anton G. Bogomolov ◽

Thomas Liehr ◽

...

Keyword(s):

Laser Scanning ◽

Spatial Organization ◽

Constitutive Heterochromatin ◽

B Chromosome ◽

B Chromosomes ◽

Laser Scanning Microscopy ◽

Field Mouse ◽

Apodemus Peninsulae ◽

Basic Set ◽

Korean Field Mouse

Korean field mouse (Apodemus peninsulae) shows a wide variation in the number of B chromosomes composed of constitutive heterochromatin. For this reason, it provides a good model to study the influence of the number of centromeres and amount of heterochromatin on spatial organization of interphase nuclei. We analyzed the three-dimensional organization of fibroblast and spermatocyte nuclei of the field mice carrying a different number of B chromosomes using laser scanning microscopy and 3D fluorescence in situ hybridization. We detected a co-localization of the B chromosomes with constitutive heterochromatin of the chromosomes of the basic set. We showed a non-random distribution of B chromosomes in the spermatocyte nuclei. Unpaired B chromosomes showed a tendency to occur in the compartment formed by the unpaired part of the XY bivalent.

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B Chromosomes in Populations of Mammals Revisited

Genes ◽

10.3390/genes9100487 ◽

2018 ◽

Vol 9 (10) ◽

pp. 487 ◽

Cited By ~ 11

Author(s):

Mladen Vujošević ◽

Marija Rajičić ◽

Jelena Blagojević

Keyword(s):

Mammalian Species ◽

B Chromosome ◽

Molecular Techniques ◽

B Chromosomes ◽

General View ◽

Protein Coding ◽

Host Parasite Interactions ◽

Quantitative Characteristics ◽

Host Parasite

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.

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Transmission rate variation among three B chromosome variants in the fish Prochilodus lineatus (Characiformes, Prochilodontidae)

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-3765201387611 ◽

2013 ◽

Vol 85 (4) ◽

pp. 1371-1377 ◽

Cited By ~ 3

Author(s):

MANOLO PENITENTE ◽

TATIANA A. VOLTOLIN ◽

JOSE A. SENHORINI ◽

JEHUD BORTOLOZZI ◽

FAUSTO FORESTI ◽

...

Keyword(s):

Transmission Rate ◽

B Chromosome ◽

B Chromosomes ◽

Rate Variation ◽

Parental Line ◽

Prochilodus Lineatus ◽

Extinction Process ◽

Cytogenetic Studies ◽

Acrocentric Chromosomes ◽

Interesting System

Cytogenetic studies were developed in Prochilodus lineatus (Valenciennes 1836), describing an interesting system of small supernumerary chromosomes. The purpose of this work is to study the frequency and morphology of B chromosomes in individuals from the parental line and the inheritance patterns of these elements in individuals obtained from controlled crosses in the species P. lineatus. The transmission rate of B chromosomes revealed a kB=0.388 for the acrocentric type, a kB=0.507 for the metacentric type and a kB=0.526 for the submetacentric type. The obtained results raise hypothesis that B-acrocentric chromosomes are involved in an extinction process in this species, while the metacentric and submetacentric supernumerary elements comprises a neutral mechanism and follows a Mendelian transmission rate.

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