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

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1177-1188 ◽  
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.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

scholarly journals Structures and stability of simple DNA repeats from bacteria

2020 ◽  
Vol 477 (2) ◽  
pp. 325-339 ◽  
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.

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

Genome ◽  
1991 ◽  
Vol 34 (5) ◽  
pp. 790-798 ◽  
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.

scholarly journals Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1014 ◽  
Author(s):  
Ana Paço ◽  
Renata Freitas ◽  
Ana Vieira-da-Silva
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Evolutionary Relationship ◽  
Repetitive Dna Sequences ◽  
Dna Remodeling ◽  
Eukaryotic Genomes ◽  
Similar Organization ◽  
Dispersed Repeats

Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.

Schistosoma mansoni: adult males and females differentially express antigens encoded by repetitive genomic DNA

Parasitology ◽  
1992 ◽  
Vol 105 (1) ◽  
pp. 63-69 ◽  
Author(s):  
A. L. Smith ◽  
M. C. Huggins ◽  
J. C. Havercroft
Keyword(s):  
Schistosoma Mansoni ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Differentially Express ◽  
Potential Surface ◽  
Differentially Expressed ◽  
Adult Males ◽  
Dna Elements ◽  
Males And Females ◽  
Repetitive Dna Elements

Two repetitive DNA sequences have been characterized from Schistosoma mansoni which were transcribed into mRNAs and translated to give two families of cross-reactive proteins. One DNA element, which was present as a 230 bp Pst I fragment was arranged in tandem arrays of at least 17 copies in the genome. The second element, which could be localized to a 1800 bp Pst I fragment, was dispersed in the genome. The 1800 bp repeat was found on the mRNA encoding the 45 kDa polypeptide precursor of a potential surface antigen. This precursor was post-translationally modified to give a 50 kDa antigen (Sm50) which was expressed from the cercaria to the adult worm and in the egg. However, a proportion of this antigen was differentially modified in females and eggs to give a 60 kDa form. Two copies of the 230 bp repeat and one copy of the 1800 bp repeat were found on a second cDNA clone. The antiserum raised against the fusion protein of this clone recognized a family of cross-reactive proteins ranging from 14 to 70 kDa in size. The members of this family were also differentially expressed between the sexes. Consequently, two families of antigens have been identified which were both encoded by repetitive DNA elements and whose members were both differentially expressed in adult male and female worms.

Repetitive DNA sequences from polyploid Elymus trachycaulus and the diploid progenitor species: detection and genomic affinity of Elymus chromatin added to wheat

Genome ◽  
1991 ◽  
Vol 34 (5) ◽  
pp. 782-789 ◽  
Author(s):  
H. Tsujimoto ◽  
B. S. Gill
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Fragment Length Polymorphism ◽  
Telomeric Sequence ◽  
Repetitive Dna Sequences ◽  
Diploid Progenitor ◽  
Specific Detection ◽  
Genome Species ◽  
Elymus Trachycaulus

A set of four repetitive DNA clones, pEt1, pEt2, pCb1, and pCb3, were isolated from SH-genome polyploid Elymus trachycaulus and H-genome diploid Critesion bogdanii. The clone Et1 represents a tandemly arranged telomeric sequence. Et2 represents tandem repeats interspersed along the entire length of individual chromosomes. The Cb1 sequence was more evenly dispersed. The Et1 clone shared homology with a 350 base pair family of rye sequences. The Cb3 sequence was evenly distributed in S- and H-genome species. All the repetitive DNA sequences were excellent markers for the specific detection and genomic affinity of Elymus chromatin added to wheat. All clones showed intragenomic variation in copy number and chromosomal location. Based on the analysis of this variation, we conclude that E. trachycaulus most probably originated from putative diploid H- and S-genome species resembling Critesion californicum and Pseudoroegneria spicata, respectively.Key words: wheatgrass, wheat–Elymus hybrid, addition lines, polyploidy, restriction fragment length polymorphism.

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

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1221-1229 ◽  
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.

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

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.

Quantitative and qualitative genomic characterization of cultivated Ilex L. species

2014 ◽  
Vol 13 (2) ◽  
pp. 142-152 ◽  
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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