Organization of the micronuclear genome of oxytricha nova.

Abstract In the hypotrichous ciliated protozoan Oxytricha nova, approximately 95% of the micronuclear genome, including all of the repetitive DNA and most of the unique sequence DNA, is eliminated during the formation of the macronuclear genome. We have examined the interspersion patterns of repetitive and unique and eliminated and retained sequences in the micronuclear genome by characterizing randomly selected clones of micronuclear DNA. Three major classes of clones have been defined: (1) those containing primarily unique, retained sequences; (2) those containing only unique, eliminated sequences; and (3) those containing only repetitive, eliminated sequences. Clones of type one and three document two aspects of organization observed previously: clustering of macronuclear destined sequences and the presence of a prevalent repetitive element. Clones of the second type demonstrate for the first time that eliminated unique sequence DNA occurs in long stretches uninterrupted by repetitive sequences. To further examine repetitive sequence interspersion, we characterized the repetitive sequence family that is present in 50% of the clones (class three above). A consensus map of this element was obtained by mapping approximately 80 phage clones and by hybridization to digests of micronuclear DNA. The repeat element is extremely large (approximately 24 kb) and is interspersed with both macronuclear destined sequences and eliminated unique sequences.

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Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing

Cytogenetic and Genome Research ◽

10.1159/000506531 ◽

2020 ◽

Vol 160 (3) ◽

pp. 141-147 ◽

Cited By ~ 1

Author(s):

Marcelo J. da Silva ◽

Raquel Fogarin Destro ◽

Thiago Gazoni ◽

Hideki Narimatsu ◽

Paulo S. Pereira dos Santos ◽

...

Keyword(s):

Repetitive Dna ◽

Sex Chromosomes ◽

Dna Sequences ◽

Satellite Dna ◽

Sex Chromosome ◽

Repetitive Sequences ◽

Centromere Function ◽

Sex Chromosome System ◽

First Time ◽

Eukaryotic Genomes

Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.

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Repetitive Sequence and Sex Chromosome Evolution in Vertebrates

Advances in Evolutionary Biology ◽

10.1155/2014/104683 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 25

Author(s):

Tariq Ezaz ◽

Janine E. Deakin

Keyword(s):

Repetitive Dna ◽

Sex Chromosomes ◽

Repetitive Sequence ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Repetitive Sequences ◽

Sex Chromosome Evolution ◽

Genomic Changes ◽

Heteromorphic Sex Chromosomes ◽

Simple Repetitive Sequences

Sex chromosomes are the most dynamic entity in any genome having unique morphology, gene content, and evolution. They have evolved multiple times and independently throughout vertebrate evolution. One of the major genomic changes that pertain to sex chromosomes involves the amplification of common repeats. It is hypothesized that such amplification of repeats facilitates the suppression of recombination, leading to the evolution of heteromorphic sex chromosomes through genetic degradation of Y or W chromosomes. Although contrasting evidence is available, it is clear that amplification of simple repetitive sequences played a major role in the evolution of Y and W chromosomes in vertebrates. In this review, we present a brief overview of the repetitive DNA classes that accumulated during sex chromosome evolution, mainly focusing on vertebrates, and discuss their possible role and potential function in this process.

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Variations of two repetitive DNA sequences in several Triticeae genomes revealed by polymerase chain reaction and sequencing

Genome ◽

10.1139/g95-160 ◽

1995 ◽

Vol 38 (6) ◽

pp. 1221-1229 ◽

Cited By ~ 13

Author(s):

Richard R.-C. Wang ◽

Jun-Zhi Wei

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Repetitive Sequence ◽

Repetitive Sequences ◽

Evolutionary Significance ◽

Repetitive Dna Sequences ◽

Chain Reaction ◽

Pcr Product ◽

Polymerase Chain ◽

Thinopyrum Elongatum

Genomes of Triticeae were analyzed using PCR with synthesized primers that were based on two published repetitive DNA sequences, pLeUCD2 (pLe2) and l-E6hcII-l (L02368), which were originally isolated from Thinopyrum elongatum. The various genomes produced a 240 bp PCR product having high homology with the repetitive DNA pLe2. The PCR fragments produced from different genomes differed mainly in amplification quantity and in base composition at 89 variable sites. On the other hand, amplification products from the primer set for L02368 were of different sizes and nucleotide sequences. These results show that the two repetitive DNA sequences have different evolutionary significance. pLe2 is present in all genomes tested, although differences in copy number and nucleotide sequence are notable. L02368 is more genome specific, i.e., fewer genomes possess this family of repetitive sequences. It was concluded that the repetitive sequence pLe2 family is an ancient one that existed in the progenitor genome prior to divergence of annual and perennial genomes. In contrast, sequences similar to L02368 have only evolved following genome divergence.Key words: repetitive sequence, PCR, genome, evolution, Thinopyrum, Triticeae.

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Comparison and Utilization of Repetitive-Element PCR Techniques for Typing Lactobacillus Isolates from the Chicken Gastrointestinal Tract

Applied and Environmental Microbiology ◽

10.1128/aem.01150-09 ◽

2009 ◽

Vol 75 (21) ◽

pp. 6764-6776 ◽

Cited By ~ 26

Author(s):

David P. Stephenson ◽

Robert J. Moore ◽

Gwen E. Allison

Keyword(s):

Gastrointestinal Tract ◽

Lactobacillus Reuteri ◽

Repetitive Element ◽

Necrotic Enteritis ◽

High Throughput Analysis ◽

Strain Diversity ◽

Disease Induction ◽

First Time ◽

Pcr Techniques ◽

Type Strains

ABSTRACT Three repetitive-element PCR techniques were evaluated for the ability to type strains of Lactobacillus species commonly identified in the chicken gastrointestinal tract. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) produced species- and strain-specific profiles for Lactobacillus crispatus, Lactobacillus gallinarum, Lactobacillus johnsonii, and Lactobacillus reuteri isolates. The technique typed strains within these species equally as well as pulsed-field gel electrophoresis. DNA concentration and quality did not affect the ERIC-PCR profiles, indicating that this method, unlike other high-resolution methods, can be adapted to high-throughput analysis of isolates. Subsequently, ERIC-PCR was used to type Lactobacillus species diversity of a large collection of isolates derived from chickens grown under commercial and necrotic enteritis disease induction conditions. This study has illustrated, for the first time, that there is great strain diversity within each Lactobacillus species present and has revealed that chickens raised under commercial conditions harbor greater species and strain diversity than chickens raised under necrotic enteritis disease induction conditions.

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A method for mapping germ line sequences in Tetrahymena thermophila using the polymerase chain reaction.

Genetics ◽

10.1093/genetics/137.1.95 ◽

1994 ◽

Vol 137 (1) ◽

pp. 95-106 ◽

Cited By ~ 1

Author(s):

D Cassidy-Hanley ◽

M C Yao ◽

P J Bruns

Keyword(s):

Polymerase Chain Reaction ◽

Dna Sequences ◽

Tetrahymena Thermophila ◽

Germ Line ◽

Repetitive Sequences ◽

Mapping Technique ◽

Ciliated Protozoan ◽

Chain Reaction ◽

Polymerase Chain ◽

Template Dna

Abstract A method for mapping DNA sequences to specific germinal chromosomes in the ciliated protozoan Tetrahymena thermophila has been developed. This mapping technique (PCR mapping) utilizes the polymerase chain reaction and template DNA derived from nullisomic strains to directly assign micronuclear DNA sequences to specific micronuclear chromosomes. Using this technique, a number of unique sequences and short repetitive sequences flanked by unique sequences have been mapped to four of the five germinal chromosomes.

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Structures and stability of simple DNA repeats from bacteria

Biochemical Journal ◽

10.1042/bcj20190703 ◽

2020 ◽

Vol 477 (2) ◽

pp. 325-339 ◽

Cited By ~ 4

Author(s):

Vaclav Brazda ◽

Miroslav Fojta ◽

Richard P. Bowater

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Genetic Instability ◽

Repetitive Sequences ◽

Biological Significance ◽

Human Diseases ◽

Repetitive Dna Sequences ◽

Dna Repeats ◽

Diverse Range ◽

Dna Structures

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

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Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and Oryza australiensis

Genome ◽

10.1139/g91-123 ◽

1991 ◽

Vol 34 (5) ◽

pp. 790-798 ◽

Cited By ~ 10

Author(s):

H. Aswidinnoor ◽

R. J. Nelson ◽

J. F. Dallas ◽

C. L. McIntyre ◽

H. Leung ◽

...

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Genomic Dna ◽

Repetitive Sequences ◽

Rice Genome ◽

Repetitive Dna Sequences ◽

Cross Hybridization ◽

Oryza Minuta ◽

Wild Rice Species ◽

Oryza Australiensis

The value of genome-specific repetitive DNA sequences for use as molecular markers in studying genome differentiation was investigated. Five repetitive DNA sequences from wild species of rice were cloned. Four of the clones, pOm1, pOm4, pOmA536, and pOmPB10, were isolated from Oryza minuta accession 101141 (BBCC genomes), and one clone, pOa237, was isolated from Oryza australiensis accession 100882 (EE genome). Southern blot hybridization to different rice genomes showed strong hybridization of all five clones to O. minuta genomic DNA and no cross hybridization to genomic DNA from Oryza sativa (AA genome). The pOm1 and pOmA536 sequences showed cross hybridization only to all of the wild rice species containing the C genome. However, the pOm4, pOmPB10, and pOa237 sequences showed cross hybridization to O. australiensis genomic DNA in addition to showing hybridization to the O. minuta genomic DNA.Key words: rice, genome-specific repetitive sequences, Oryza.

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Evolutionary characterization of a Y chromosomal sequence conserved in the genus Mus

Genetics Research ◽

10.1017/s001667230002752x ◽

1988 ◽

Vol 52 (2) ◽

pp. 145-150 ◽

Cited By ~ 5

Author(s):

Yutaka Nishioka

Keyword(s):

Related Species ◽

Rattus Norvegicus ◽

Phylogenetic Relationships ◽

Repetitive Sequence ◽

Repetitive Sequences ◽

Closely Related Species ◽

Specific Hybridization ◽

Male Specific ◽

Chromosomal Sequence

SummaryThe extent of accumulation of mouse Y chromosomal repetitive sequences generally correlates with the known phylogenetic relationships in the genus Mus. However, we describe here a M. musculus Y chromosomal repetitive sequence, designated as ACClfl, whose accumulation patterns among eight Mus species do not correspond to their phylogenetic relationships. Although male-specific hybridization bands were present in all the species examined, significant accumulation (> 200 copies) in the Y chromosomes was found in M. minutoides (subgenus Nannomys), M. pahari (subgenus Coelomys) and M. saxicola (subgenus Pyromys) as well as in the three closely related species M. hortulanus, M. musculus and M. spretus that belong to the subgenus Mus. Unexpectedly, the Y chromosomes of M. caroli and M. cookii (both subgenus Mus) had considerably reduced amounts of ACClfl-related sequences. Furthermore, in rats (Rattus norvegicus) the major accumulation sites appear to be autosomal. These observations suggest that caution must be taken in the interpretation of data obtained with repetitive sequences that have evolved quickly.

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