The Repetitive DNA Content of Eukaryotic Genomes

2012 ◽  
pp. 1-28 ◽  
Author(s):  
I. López-Flores ◽  
M.A. Garrido-Ramos
Keyword(s):  
Repetitive Dna ◽  
Dna Content ◽  
Eukaryotic Genomes

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.

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.

Low repetitive DNA content in Aspergillus nidulans

Science ◽  
1978 ◽  
Vol 202 (4371) ◽  
pp. 973-975 ◽  
Author(s):  
W. Timberlake
Keyword(s):  
Aspergillus Nidulans ◽  
Repetitive Dna ◽  
Dna Content

Repetitive DNA in ThreeGramineaeSpecies with Low DNA Content

1980 ◽  
Vol 361 (2) ◽  
pp. 1223-1234 ◽  
Author(s):  
Vidya G. DESHPANDE ◽  
Prabhakar K. RANJEKAR
Keyword(s):  
Repetitive Dna ◽  
Dna Content

scholarly journals A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes

1997 ◽  
Vol 7 (5) ◽  
pp. 551-563 ◽  
Author(s):  
Scott E. Devine ◽  
Stephanie L. Chissoe ◽  
Yolanda Eby ◽  
Richard K. Wilson ◽  
Jef D. Boeke
Keyword(s):  
Repetitive Dna ◽  
Eukaryotic Genomes

Abundance and variation of microsatellite DNA sequences in beans (Phaseolus andVigna)

Genome ◽  
1999 ◽  
Vol 42 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Kangfu Yu ◽  
Soon J Park ◽  
Vaino Poysa
Keyword(s):  
Common Bean ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Allelic Variation ◽  
Pcr Analysis ◽  
Or Groups ◽  
Recombinant Inbred Population ◽  
Nucleotide Repeats ◽  
Eukaryotic Genomes ◽  
Simple Sequence

Microsatellites or simple sequence repeats (SSRs) have been demonstrated to be abundant and hypervariable in some eukaryotic genomes. Although the presence of microsatellites is very well documented in many plant species, no information on microsatellites in beans (Phaseolus andVigna) is available. To assess the abundance and usefulness of bean microsatellites as genetic markers, 326 DNA sequences from the GenBank databases were searched. Sixty-one simple repetitive DNA sequences with 23 different types of repetitive DNA motifs were identified as potential microsatellites. Among these were 49 microsatellites from common bean (Phaseolus vulgaris) entries and 12 microsatellites from the genus Vigna. The most abundant type of microsatellite found in this search was that with di-nucleotide repeats of AT/TA. Microsatellites with tri- and tetra-nucleotide motifs were also identified. PCR analysis of 12 of the microsatellite-containing loci revealed that 11 of the 12 primer pairs could produce easily-scorable fragments, or groups of fragments. Allelic variation of the 11 loci was surveyed in 12 common bean inbred lines representing a diversity of germplasms. Seven of the 11 microsatellite loci were polymorphic and yielded 2-10 alleles. Analyses of the polymorphic loci in a common bean F6 recombinant inbred population showed that each segregated in a Mendelian fashion.Key words: microsatellite, simple sequence repeat, molecular marker, bean.

scholarly journals Tissue homogeneity requires inhibition of unequal gene silencing during development

2016 ◽  
Vol 214 (3) ◽  
pp. 319-331 ◽  
Author(s):  
Hai H. Le ◽  
Monika Looney ◽  
Benjamin Strauss ◽  
Michael Bloodgood ◽  
Antony M. Jose
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Gene Silencing ◽  
Repetitive Dna ◽  
Dna Content ◽  
Intestinal Cells ◽  
Cellular Processes ◽  
Cell Divisions ◽  
Developmental Mechanisms ◽  
Multicellular Organisms

Multicellular organisms can generate and maintain homogenous populations of cells that make up individual tissues. However, cellular processes that can disrupt homogeneity and how organisms overcome such disruption are unknown. We found that ∼100-fold differences in expression from a repetitive DNA transgene can occur between intestinal cells in Caenorhabditis elegans. These differences are caused by gene silencing in some cells and are actively suppressed by parental and zygotic factors such as the conserved exonuclease ERI-1. If unsuppressed, silencing can spread between some cells in embryos but can be repeat specific and independent of other homologous loci within each cell. Silencing can persist through DNA replication and nuclear divisions, disrupting uniform gene expression in developed animals. Analysis at single-cell resolution suggests that differences between cells arise during early cell divisions upon unequal segregation of an initiator of silencing. Our results suggest that organisms with high repetitive DNA content, which include humans, could use similar developmental mechanisms to achieve and maintain tissue homogeneity.

Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust

Chromosoma ◽  
2017 ◽  
Vol 127 (1) ◽  
pp. 45-57 ◽  
Author(s):  
Francisco J. Ruiz-Ruano ◽  
Josefa Cabrero ◽  
María Dolores López-León ◽  
Antonio Sánchez ◽  
Juan Pedro M. Camacho
Keyword(s):  
Repetitive Dna ◽  
Dna Content ◽  
Supernumerary Chromosome ◽  
Migratory Locust ◽  
Sequence Characterization

scholarly journals Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 72 ◽  
Author(s):  
Sandra Louzada ◽  
Mariana Lopes ◽  
Daniela Ferreira ◽  
Filomena Adega ◽  
Ana Escudeiro ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Current Knowledge ◽  
Genome Architecture ◽  
Genome Plasticity ◽  
Turnover Rates ◽  
High Turnover ◽  
Satellite Dnas ◽  
Genomic Technologies ◽  
Eukaryotic Genomes

Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.

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