Genome analysis and replication behavior of a set of repetitive sequences of Lilium longiflorum

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 535-541
Author(s):  
Nishan Jayawardene ◽  
C. Daniel Riggs ◽  
Clare A. Hasenkampf
Keyword(s):  
Dna Replication ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genome Analysis ◽  
Repetitive Sequences ◽  
Genome Structure ◽  
Lilium Longiflorum ◽  
Chromosome Homology ◽  
Replication Assay ◽  
Expected Increase

The four clones, pLZH47, pLZ112, pLZ113, and pLZ122, previously assumed to contain DNA sequences that replicate during zygotene (zygDNA), actually had their replication behavior tested using a replication assay. Genome analysis was also done for each clone. All of the clones seem to be members of families of dispersed repetitive DNA. The number of copies per 2C genome are as follows: pLZH47, 13 500; pLZ112, >100; pLZ113, 200; and pLZ122, 3500. The replication assays measured the amount of hybridizable sequences available at the stage of leptotene (before zygotene DNA replication occurs) and at the stage of pachytene (after zygotene replication occurs). True zygDNA clones should have twice as many sequences to hybridize to at pachytene as at leptotene. None of the clones had the expected increase. One clone, pLZ122, did show a statistically significant increase (10%). It may consist of a mixture of zygDNA and non-zygDNA sequences. Alternatively, only 10% of the pLZ122 family members may function as zygDNA.Key words: meiosis, zygDNA sequences, synapsis, chromosome homology, genome structure.

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.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 710-717 ◽  
Author(s):  
B. Kolano ◽  
B.W. Gardunia ◽  
M. Michalska ◽  
A. Bonifacio ◽  
D. Fairbanks ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chenopodium Quinoa ◽  
5S Rdna ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

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

2020 ◽  
Vol 160 (3) ◽  
pp. 141-147 ◽  
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.

The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae

2015 ◽  
Vol 147 (2-3) ◽  
pp. 161-168 ◽  
Author(s):  
Natalia D.M. Carvalho ◽  
Vanessa S.S. Pinheiro ◽  
Edson J. Carmo ◽  
Leonardo G. Goll ◽  
Carlos H. Schneider ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genome Organization ◽  
Repetitive Sequences ◽  
5S Rdna ◽  
Distinct Pattern ◽  
Structural Function ◽  
Mitotic Chromosomes ◽  
Lizard Species ◽  
Evolutionary Diversification

Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements Rex1 and SINE) of mitotic chromosomes of Amazonian species of teiids (Ameiva ameiva, Cnemidophorus sp. 1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin) to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in Cnemidophorus sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.

Possible repetitive DNA markers for Eusorghum and Parasorghum and their potential use in examining phylogenetic hypotheses on the origin of Sorghum species

Genome ◽  
1991 ◽  
Vol 34 (2) ◽  
pp. 241-250 ◽  
Author(s):  
Hoang-Tang ◽  
Shyam K. Dube ◽  
George H. Liang ◽  
Shain-Dow Kung
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Meiotic Chromosome ◽  
Repetitive Sequences ◽  
Copy Numbers ◽  
Major Species ◽  
Strong Homology ◽  
Genome Phylogeny ◽  
Genomic Dnas ◽  
Phylogenetic Hypotheses

Genomic structures of two major species in section Eusorghum (Sorghum), Sorghum bicolor and Sorghum halepense, and their phylogenetic relationships with a species in section Parasorghum, Sorghum versicolor, were studied by using cloned repetitive DNA sequences from the three species. Of the five repetitive DNA clones isolated from S. bicolor and S. halepense, four produced qualitatively similar hybridization patterns with detectable variations in copy numbers of some of the restriction fragments on the Southern blots of the two genomic DNAs. One clone was shown to be diagnostic for S. halepense. Molecular analysis at the DNA level indicates that S. bicolor and S. halepense have similar but not identical genomes, consonant with differences in karyotypes, meiotic chromosome behaviors, morphology, and physiology of the species. In addition to five repetitive clones isolated from S. bicolor and S. halepense, eight more sequences were cloned from S. versicolor. Nine clones were found to be specific for either S. bicolor and S. halepense or S. versicolor. The remaining four had a moderate to strong homology with sequences present in all Sorghum species studied. We speculate that the genome in the common ancestor of Sorghum has differentiated to give rise to genomes of at least three major chromosome sizes; large, medium, and small, as seen at present. Amplifications, eliminations, rearrangements, and new syntheses of repetitive sequences may have been involved in genome differentiation of these species. The results also suggest that the S. versicolor genome has strongly diverged from the genomes of the two species in section Eusorghum.Key words: repetitive DNA, genome, phylogeny, Eusorghum, Parasorghum, Sorghum.

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.

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