Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and 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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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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Molecular characterization and chromosomal distribution of species-specific repetitive DNA sequences from Beta corolliflora, a wild relative of sugar beet

Genome ◽

10.1139/g00-084 ◽

2000 ◽

Vol 43 (6) ◽

pp. 1073-1080 ◽

Cited By ~ 17

Author(s):

D Gao ◽

T Schmidt ◽

C Jung

Keyword(s):

Sugar Beet ◽

Repetitive Dna ◽

Dna Sequences ◽

Genomic Dna ◽

Southern Hybridization ◽

Repetitive Dna Sequences ◽

Wild Relative ◽

Chromosomal Distribution ◽

Species Specific ◽

Specific Sequences

Repetitive DNA sequences have been isolated from a Sau3AI plasmid library of tetraploid Beta corolliflora (2n = 4x = 36), a wild relative of sugar beet (B. vulgaris). The library was screened by differential hybridization with genomic DNA of B. corolliflora and B. vulgaris. When used as probes for Southern hybridization of genomic DNA, six clones were determined to represent highly repetitive DNA families present only in the B. corolliflora genome. Five other sequences were highly repetitive in B. corolliflora and low or single copy in B. vulgaris. The insert size varied between 43 bp and 448 bp. Two sequences pBC1279 and pBC1944 displayed strong homology to a previously cloned satellite DNA from B. nana. With one exception, sequences are tandemly arranged as revealed by a typical ladder pattern after genomic Southern hybridization. The chromosomal distribution of five probes was determined by fluorescence in situ hybridization (FISH) of mitotic metaphases from B. corolliflora and a triploid hybrid between B. vulgaris and B. corolliflora. Three sequences were spread along all chromosome arms of B. corolliflora while one sequence was present on only six chromosomes. The chromosome-specific sequence pBC216 was found in close vicinity to the 5S rDNA located on B. corolliflora chromosome IV. This set of species-specific sequences has the potential to be used as probes for the identification of monosomic alien addition lines and for marker-assisted gene transfer from wild beet to cultivated beet.Key words: Beta vulgaris, FISH, repetitive DNA, species-specific sequences.

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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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Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

10.1101/2020.08.24.264986 ◽

2020 ◽

Author(s):

Mariela Sader ◽

Magdalena Vaio ◽

Luiz Augusto Cauz-Santos ◽

Marcelo Carnier Dornelas ◽

Maria Lucia Carneiro Vieira ◽

...

Keyword(s):

Genome Size ◽

Repetitive Dna ◽

Dna Sequences ◽

Large Scale ◽

Repetitive Sequences ◽

Size Variation ◽

Repetitive Dna Sequences ◽

Ltr Retrotransposons ◽

Genome Size Variation ◽

Satellite Dnas

ABSTRACTRepetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs.MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

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Relationship between methylation of middle-repetitive DNA sequences in inducer-sensitive and resistant clones of Friend erythroleukemia cells and synthesis of poly(A)+RNA containing homologous repetitive sequences

Gene ◽

10.1016/0378-1119(88)90271-5 ◽

1988 ◽

Vol 74 (1) ◽

pp. 143-145

Author(s):

Natalie Schneiderman ◽

Chang Zee-Fen ◽

Judith K. Christman

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Repetitive Sequences ◽

Repetitive Dna Sequences ◽

Erythroleukemia Cells ◽

Friend Erythroleukemia Cells

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Quantitative and qualitative genomic characterization of cultivated Ilex L. species

Plant Genetic Resources ◽

10.1017/s1479262114000756 ◽

2014 ◽

Vol 13 (2) ◽

pp. 142-152 ◽

Cited By ~ 4

Author(s):

Alexandra Marina Gottlieb ◽

Lidia Poggio

Keyword(s):

Genome Size ◽

Repetitive Dna ◽

Dna Sequences ◽

Sequence Data ◽

Repetitive Sequences ◽

Representational Difference Analysis ◽

Ilex Paraguariensis ◽

Repetitive Dna Sequences ◽

A Genome

The development of modern approaches to the genetic improvement of the tree crops Ilex paraguariensis (‘yerba mate’) and Ilex dumosa (‘yerba señorita’) is halted by the scarcity of basic genetic information. In this study, we characterized the implementation of low-cost methodologies such as representational difference analysis (RDA), single-strand conformation polymorphisms (SSCP), and reverse and direct dot-blot filter hybridization assays coupled with thorough bioinformatic characterization of sequence data for both species. Also, we estimated the genome size of each species using flow cytometry. This study contributes to the better understanding of the genetic differences between two cultivated species, by generating new quantitative and qualitative genome-level data. Using the RDA technique, we isolated a group of non-coding repetitive sequences, tentatively considered as Ilex-specific, which were 1.21- to 39.62-fold more abundant in the genome of I. paraguariensis. Another group of repetitive DNA sequences involved retrotransposons, which appeared 1.41- to 35.77-fold more abundantly in the genome of I. dumosa. The genomic DNA of each species showed different performances in filter hybridizations: while I. paraguariensis showed a high intraspecific affinity, I. dumosa exhibited a higher affinity for the genome of the former species (i.e. interspecific). These differences could be attributed to the occurrence of homologous but slightly divergent repetitive DNA sequences, highly amplified in the genome of I. paraguariensis but not in the genome of I. dumosa. Additionally, our hybridization outcomes suggest that the genomes of both species have less than 80% similarity. Moreover, for the first time, we report herein a genome size estimate of 1670 Mbp for I. paraguariensis and that of 1848 Mbp for I. dumosa.

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Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa

Genome ◽

10.1139/g01-148 ◽

2002 ◽

Vol 45 (2) ◽

pp. 431-441 ◽

Cited By ~ 17

Author(s):

Evgueni V Ananiev ◽

M Isabel Vales ◽

Ronald L Phillips ◽

Howard W Rines

Keyword(s):

In Situ Hybridization ◽

Repetitive Dna ◽

Dna Sequences ◽

Avena Sativa ◽

Genomic Dna ◽

Repetitive Sequences ◽

Repeated Sequences ◽

C Genome ◽

Copy Dna

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.Key words: oat, cosmid library, in situ hybridization.

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Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.)

Genome ◽

10.1139/g95-156 ◽

1995 ◽

Vol 38 (6) ◽

pp. 1177-1188 ◽

Cited By ~ 15

Author(s):

Xinping Zhao ◽

Rod A. Wing ◽

Andrew H. Paterson

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Tandem Repeats ◽

Repetitive Sequences ◽

Repetitive Dna Sequences ◽

Tetraploid Cotton ◽

Cotton Genome ◽

Cotton Species ◽

Dna Elements ◽

Repetitive Dna Elements

Repetitive DNA elements representing 60–70% of the total repetitive DNA in tetraploid cotton (Gossypium barbadense L.) and comprising 30–36% of the tetraploid cotton genome were isolated from a genomic library of DNA digested with a mixture of four blunt-end cutting restriction enzymes. A total of 313 clones putatively containing nuclear repetitive sequences were classified into 103 families, based on cross hybridization and Southern blot analysis. The 103 families were characterized in terms of genome organization, methylation pattern, abundance, and DNA variation. As in many other eukaryotic genomes, interspersed repetitive elements are the most abundant class of repetitive DNA in the cotton genome. Paucity of tandem repeat families with high copy numbers (>104) may be a unique feature of the cotton genome as compared with other higher plant genomes. Interspersed repeats tend to be methylated, while tandem repeats seem to be largely unmethylated in the cotton genome. Minimal variation in repertoire and overall copy number of repetitive DNA elements among different tetraploid cotton species is consistent with the hypothesis of a relatively recent origin of tetraploid cottons.Key words: genome analysis, genome evolution, tandemly repetitive DNA sequences, interspersed repetitive DNA sequences, polyploid.

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