scholarly journals Origin, Behaviour, and Transmission of B Chromosome with Special Reference to Plantago lagopus

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 152 ◽  
Author(s):  
Manoj Dhar ◽  
Jasmeet Kour ◽  
Sanjana Kaul
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
B Chromosome ◽  
Repetitive Elements ◽  
B Chromosomes ◽  
Current Status ◽  
Sequencing Data ◽  
Molecular Cytogenetic Techniques ◽  
Plantago Lagopus ◽  
Eukaryotic Organisms

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.

scholarly journals Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes)

2015 ◽  
Vol 146 (4) ◽  
pp. 311-318 ◽  
Author(s):  
Sandro N. Daniel ◽  
Manolo Penitente ◽  
Duílio M.Z.A. Silva ◽  
Diogo T. Hashimoto ◽  
Daniela C. Ferreira ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
B Chromosome ◽  
Gene Probe ◽  
Histone Genes ◽  
Chromosomal Distribution ◽  
Evolutionary Mechanisms ◽  
Small Sites ◽  
Eukaryotic Organisms

An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.

Remersonia, a new genus for Stilbella thermophila, a thermophilic mould from compost

1997 ◽  
Vol 75 (7) ◽  
pp. 1158-1165 ◽  
Author(s):  
Keith A. Seifert ◽  
Gerry Louis-Seize ◽  
Robert A. Samson ◽  
Teun Boekhout
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
New Genus ◽  
Cladistic Analysis ◽  
Thermophilic Fungi ◽  
Sequencing Data ◽  
Mushroom Compost ◽  
Supplementary Material ◽  
28S Ribosomal Dna ◽  
Partial 18S

The thermophilic synnematous hyphomycete Stilbella thermophila is redescribed and illustrated based on the study of type and supplementary material. The species is transferred to a new anamorph genus, Remersonia, characterized by determinate synnemata with scarcely branched conidiophores, percurrently proliferating conidiogenous cells, relatively large ameroconidia that accumulate in slime, and thermotolerant growth. Cladistic analysis of partial 18S and 28S ribosomal DNA sequences suggest that the fungus is a member of the Sordariales. Septal ultrastructure and a failure to grow on benomyl-emended media support the ascomycetous affinities of the fungus. Failure to grow on cycloheximide-emended media supports sequencing data suggesting that the species is not allied with the Ophiostomatales. The biology of the fungus is briefly discussed. Key words: thermophilic fungi, mushroom compost, hyphomycetes, systematics, 18S rDNA, 28S rDNA.

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

2016 ◽  
Vol 148 (1) ◽  
pp. 68-73 ◽  
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.

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

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.

scholarly journals Data Structures to Represent a Set of k -long DNA Sequences

2021 ◽  
Vol 54 (1) ◽  
pp. 1-22
Author(s):  
Rayan Chikhi ◽  
Jan Holub ◽  
Paul Medvedev
Keyword(s):  
Data Structures ◽  
Dna Sequences ◽  
Sequencing Data ◽  
String Algorithms ◽  
Fixed Length ◽  
The Past

The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k -mers, which are short fixed-length strings present in a dataset. While these approaches are rather diverse, storing and querying a k -mer set has emerged as a shared underlying component. A set of k -mers has unique features and applications that, over the past 10 years, have resulted in many specialized approaches for its representation. In this survey, we give a unified presentation and comparison of the data structures that have been proposed to store and query a k -mer set. We hope this survey will serve as a resource for researchers in the field as well as make the area more accessible to researchers outside the field.

Phylogenetic Analysis of Trichaptum Based on Nuclear 18S, 5.8S and ITS Ribosomal DNA Sequences

Mycologia ◽  
1997 ◽  
Vol 89 (5) ◽  
pp. 727 ◽  
Author(s):  
Kwan S. Ko ◽  
Soon G. Hong ◽  
Hack S. Jung
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences

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

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rahman Ebrahimzadegan ◽  
Andreas Houben ◽  
Ghader Mirzaghaderi
Keyword(s):  
Repetitive Sequences ◽  
Nuclear Genome ◽  
B Chromosome ◽  
B Chromosomes ◽  
Festuca Pratensis ◽  
Ltr Retrotransposons ◽  
Chromosome Identification ◽  
Satellite Repeats ◽  
Low Pass ◽  
Illumina Sequence

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.

scholarly journals Leishmaniasis: Current Status of Vaccine Development

2001 ◽  
Vol 14 (2) ◽  
pp. 229-243 ◽  
Author(s):  
Emanuela Handman
Keyword(s):  
Dna Sequences ◽  
Vaccine Development ◽  
Development Program ◽  
Skin Lesions ◽  
Mononuclear Phagocytes ◽  
Control Measures ◽  
Host Susceptibility ◽  
Current Status ◽  
Dna Encoding ◽  
And Control

SUMMARY Leishmaniae are obligatory intracellular protozoa in mononuclear phagocytes. They cause a spectrum of diseases, ranging in severity from spontaneously healing skin lesions to fatal visceral disease. Worldwide, there are 2 million new cases each year and 1/10 of the world's population is at risk of infection. To date, there are no vaccines against leishmaniasis and control measures rely on chemotherapy to alleviate disease and on vector control to reduce transmission. However, a major vaccine development program aimed initially at cutaneous leishmaniasis is under way. Studies in animal models and humans are evaluating the potential of genetically modified live attenuated vaccines, as well as a variety of recombinant antigens or the DNA encoding them. The program also focuses on new adjuvants, including cytokines, and delivery systems to target the T helper type 1 immune responses required for the elimination of this intracellular organism. The availability, in the near future, of the DNA sequences of the human and Leishmania genomes will extend the vaccine program. New vaccine candidates such as parasite virulence factors will be identified. Host susceptibility genes will be mapped to allow the vaccine to be targeted to the population most in need of protection.

scholarly journals Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

2013 ◽  
Vol 72 (1) ◽  
pp. 1-133 ◽  
Author(s):  
Višnja Besendorfer ◽  
Jelena Mlinarec
Keyword(s):  
Dna Sequences ◽  
Southern Hybridization ◽  
Repeat Unit ◽  
Similar Species ◽  
Genomic Component ◽  
Library Hypothesis ◽  
Species Specific ◽  
Eukaryotic Organisms ◽  
Fish Signal

Abstract Satellite DNAis a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNAis an important element in genome organization and evolution in plants. Here we study the presence, physical distribution and abundance of the satellite DNAfamily AhTR1 in Anemone. Twenty-two Anemone accessions were analyzed by PCR to assess the presence of AhTR1, while fluorescence in situ hybridization and Southern hybridization were used to determine the abundance and genomic distribution of AhTR1. The AhTR1 repeat unit was PCR-amplified only in eight phylogenetically related European Anemone taxa of the Anemone section. FISH signal with AhTR1 probe was visible only in A. hortensis and A. pavonina, showing localization of AhTR1 in the regions of interstitial heterochromatin in both species. The absence of a FISH signal in the six other taxa as well as weak signal after Southern hybridization suggest that in these species AhTR1 family appears as relict sequences. Thus, the data presented here support the »library hypothesis« for AhTR1 satellite evolution in Anemone. Similar species-specific satellite DNAprofiles in A. hortensis and A. pavonina support the treatment of A. hortensis and A. pavonina as one species, i.e. A. hortensis s.l.

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