Repeated DNA sequences as an engine of biological diversification

Grechko, V. V.

doi:10.1134/s0026893311050050

Cited by 11 publications

(8 citation statements)

References 181 publications

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“…Our study demonstrates that this is not true. All phylogenetic reconstructions based on highly repetitive noncoding DNA follow the conse quence of evolutionary events known for the model organisms in question (for a review, see [50]). While the fish groups chosen for the study substantially differ in main evolutionary stages and divergence time [33,34,[51][52][53][54][55], an integral genome analysis, which simultaneously addresses many anonymous loci, makes it possible to reduce the inequality errors caused by the differences in the molecular evolution rates of macromolecules [56].…”

Section: Reaction With 31smmentioning

confidence: 99%

Repetitive DNA sequences as an indicator of the level of genetic isolation in fish

et al. 2015

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Although the functional role is still unknown for most types of nuclear noncoding repetitive sequences, some of them proved to provide adequate phylogenetic and taxonomic markers for studying the genetic relationships of organisms at the species and within species levels. Several markers were used in this work. First, microsatellite markers were used to examine populations varying in the extent of genetic subdi vision in marine and anadromous fish, including the Chilean jack mackerel Trachurus murphyi, anadromous brown trout Salmo trutta, and isolated and anadromous char populations. Locus polymorphism was propor tional to the gene flow between populations in all cases. Second, satellite DNA was used to study the phylo genetic relationships within the genera Salmo, Oncorhynchus, Salvelinus, and Coregonus. Genetic distances agreed well with the taxonomic relationships based on morphological traits and various biochemical markers and correlated with the evolutionary ages estimated for the groups by other markers. Third, RAPD PCR with a set of 20 mer primers was performed to study the genus Coregonus and anadromous and isolated popula tions and species of the genus Salvelinus. The resulting phylogenetic trees may help to resolve some disputable taxonomic issues for the groups. A comparison showed that several RAPD detected sequences contain con served fragments of coding sequences and polymorphic repeats (minisatellites) from intergenic regions or introns. The finding point to a nonrandom nature of repetitive DNA divergence and may reflect the evolution of the fish groups examined. Heterochromatic satellite repeats were assumed to contribute to generating a reproductive barrier.

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Section: Reaction With 31smmentioning

confidence: 99%

Repetitive DNA sequences as an indicator of the level of genetic isolation in fish

et al. 2015

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“…Secondly, SAARs (Single Amino Acid Repeats) also known as “Homopeptides” (a special type of direct repeats with no spacer sequence) are repeats that are formed by a single amino acid being repeated in tandem and are believed to arise due to the sequential expansion of short codons in the genome. These repeats have also often associated with regulatory network of epigenesis, replication, transcription and evolution [ 3 , 16 ]. In addition, they are linked to the development and activity of a peripheral nervous system [ 17 ] and with diseases like Huntington disease and other nervous system related diseases.…”

Section: Introductionmentioning

confidence: 99%

PPS: A computing engine to find Palindromes in all Protein sequences

et al. 2014

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The primary structure of a protein molecule comprises a linear chain of amino acid residues. Certain parts of this linear chain are unique in nature and function. They can be classified under different categories and their roles studied in detail. Two such unique categories are the palindromic sequences and the Single Amino Acid Repeats (SAARs), which plays a major role in the structure, function and evolution of the protein molecule. In spite of their presence in various protein sequences, palindromes have not yet been investigated in detail. Thus, to enable a comprehensive understanding of these sequences, a computing engine, PPS, has been developed. The users can search the occurrences of palindromes and SAARs in all the protein sequences available in various databases and can view the three-dimensional structures (in case it is available in the known three-dimensional protein structures deposited to the Protein Data Bank) using the graphics plug-in Jmol. The proposed server is the first of its kind and can be freely accessed through the World Wide Web.AvailabilityURL http://pranag.physics.iisc.ernet.in/pps/

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“…A diametrically opposite view has been presented by other authors. Grechko (2011) considered that 'the regulation and plasticity of the genome is determined by the structure, plasticity, and evolution of genomic satellite and dispersed repetitive element, which, being tightly bound, with life phylogeny, result in somatic and inherited changes'. Similarly, Mravinac & Plohl (2010) reported that 'it becomes evident that comprehension of genomes in their entirety depends on research of repetitive DNAs'.…”

Section: Introductionmentioning

confidence: 99%

“…However, stDNA may also be strain specific with all the repeat units of one stDNA family very similar or even identical to the individual or population level, as a result of concerted evolution. The divergence generally increases with distance between taxa (review in Palomeque & Lorite, 2008; Grechko, 2011). In general, there is no conservation of stDNA families at taxonomic levels higher than genus, although some exceptions have been reported.…”

Section: Introductionmentioning

confidence: 99%

Characterization of two unrelated satellite DNA families in the Colorado potato beetleLeptinotarsa decemlineata(Coleoptera, Chrysomelidae)

Lorite

Torres

Palomeque

2013

Bull. Entomol. Res.

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The Colorado potato beetle (Leptinotarsa decemlineata, family Chrysomelidae),a phytophagous insect, which feeds preferably on potatoes, constitutes a serious pest of this crop and causes extensive damage to tomatoes and egg plants. It has a remarkable ability to develop resistance quickly against insecticides and shows a diversified and flexible life history. Consequently, the control of this pest has become difficult, requiring the development of new alternative biotechnology-based strategies. Such strategies require a thorough knowledge of the beetle’s genome,including the repetitive DNA. Satellite DNA (stDNA), composed of long arrays of tandemly arranged repeat units, constitutes the major component of heterochromatin and is located mainly in centromeric and telomeric chromosomal regions. We have studied two different unrelated satellite-DNA families of which the consensus sequences were 295 and 109bp in length, named LEDE-I and LEDE-II, respectively.Both were AT-rich (70.8% and 71.6%, respectively). Predictive models of sequence-dependent DNA bending and the study of electrophoretic mobility on non-denaturing polyacrylamide gels have shown that the DNA was curved in both satellite-DNA families. Among other features, the chromosome localization of both stDNAs has been studied. In situ hybridization performed on meiotic and mitoticnuclei showed chromosomes, including the X chromosome, with zero, one, or two stDNAs. In recent years, it has been proposed that the repetitive DNA may play a key role in biological diversification processes. This is the first molecular and cytogenetic study conducted on L. decemlineata repetitive DNA and specifically on stDNA, which is one of the important constituents of eukaryotic genomes.

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Repeated DNA sequences as an engine of biological diversification

Cited by 11 publications

References 181 publications

Repetitive DNA sequences as an indicator of the level of genetic isolation in fish

Repetitive DNA sequences as an indicator of the level of genetic isolation in fish

PPS: A computing engine to find Palindromes in all Protein sequences

Characterization of two unrelated satellite DNA families in the Colorado potato beetleLeptinotarsa decemlineata(Coleoptera, Chrysomelidae)

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