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 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.

scholarly journals PvB3s: Genome-wide and Transcriptome-wide Identification and Analysis Reveals the B3 Family Regulate Auxin to Resist Salt Stress at the Sprout Stage in Common Bean(P. Vulgaris L. ) .

2020 ◽  
Author(s):  
Qi Zhang ◽  
Wei-jia Li ◽  
Wen-jing Zhang ◽  
Zhen-gong Yin ◽  
Yu-xin Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Common Bean ◽  
Dna Sequences ◽  
Functional Characterization ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Genes Expression ◽  
Intron Structure ◽  
Auxin Content

Abstract Background: B3 gene family is a transcription factor family unique to plants, which play an important role in plant growth and development by binding specific DNA sequences. However, data on the B3 genes in the common bean and participate in many abiotic stresses especially salt stress are limited. Result: A total of encoding 100 proteins were identified in common bean. Phylogenetic analysis showed that PvB3s were classified into 4 subgroups, and these clusters were supported by several group-specific features, including exon/intron structure, MEME motifs, and predicted binding site structure. Collinearity analysis showed the connection of PvB3s in the same species and different species. The genes expression pattern showed that PvB3s expressed with a tissue-specific manner during sprout stage. Through RNA-seq and qRT-PCR analysis, it was found that there were differences in expression in extreme materials under salt stress. The determination of auxin content and the analysis of PvB3s expression in the enriched pathway showed that PvB3s would respond to auxin to enhance salt tolerance in common bean sprouting stage. Conclusion: The results provided useful and rich resources of PvB3s for the functional characterization and understanding of B3 transcription factors (TFs) in common bean, which further provides insights that PvB3s may respond to auxin to enhance salt tolerance of common bean.

Maize simple repetitive DNA sequences: abundance and allele variation

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 866-873 ◽  
Author(s):  
E. C. L. Chin ◽  
H. Shu ◽  
J. S. C. Smith ◽  
M. L. Senior
Keyword(s):  
Dna Sequences ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Inbred Lines ◽  
Agarose Gels ◽  
Maize Germplasm ◽  
Mammalian Genomes ◽  
Key Words Maize ◽  
Allele Variation ◽  
Simple Sequence

Microsatellites or simple sequence repeats, first demonstrated in human and other mammalian genomes, are being identified in many plant species. A database survey of 576 maize sequences from the GenBank and EMBL databases was made to determine the abundance of maize microsatellites. Two hundred potential microsatellites were identified. The relative abundance of the different repetitive motifs varied considerably and all possible dinucleotide and trinucleotide motif types were found. The three most abundant classes of microsatellites identified in this search were (AG/CT)n, (CCT/GGA)n, and (CCG/GGC)n repeats. Allelic variation was surveyed with 9 maize inbred lines representing diverse pedigrees. Amplification of DNA from these lines and analysis using high resolution agarose gels showed that 69 of the 200 potential microsatellites were polymorphic and yielded 2–4 alleles. A more complete screen of these loci against a wider array of maize germplasm using denaturing sequencing gels is now being conducted to more thoroughly evaluate these loci. Key words : maize, microsatellites, simple sequence repeat, molecular marker.

scholarly journals CAG Expansions Are Genetically Stable and Form Nontoxic Aggregates in Cells Lacking Endogenous Polyglutamine Proteins

mBio ◽  
2016 ◽  
Vol 7 (5) ◽  
Author(s):  
Ashley A. Zurawel ◽  
Ruth Kabeche ◽  
Sonja E. DiGregorio ◽  
Lin Deng ◽  
Kartikeya M. Menon ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genetic Instability ◽  
Growth Defect ◽  
Pcr Analysis ◽  
Repetitive Dna Sequences ◽  
Stark Contrast ◽  
Almost All ◽  
Evolutionary Emergence

ABSTRACT Proteins containing polyglutamine (polyQ) regions are found in almost all eukaryotes, albeit with various frequencies. In humans, proteins such as huntingtin (Htt) with abnormally expanded polyQ regions cause neurodegenerative diseases such as Huntington’s disease (HD). To study how the presence of endogenous polyQ aggregation modulates polyQ aggregation and toxicity, we expressed polyQ expanded Htt fragments (polyQ Htt) in Schizosaccharomyces pombe . In stark contrast to other unicellular fungi, such as Saccharomyces cerevisiae , S. pombe is uniquely devoid of proteins with more than 10 Q repeats. We found that polyQ Htt forms aggregates within S. pombe cells only with exceedingly long polyQ expansions. Surprisingly, despite the presence of polyQ Htt aggregates in both the cytoplasm and nucleus, no significant growth defect was observed in S. pombe cells. Further, PCR analysis showed that the repetitive polyQ-encoding DNA region remained constant following transformation and after multiple divisions in S. pombe , in contrast to the genetic instability of polyQ DNA sequences in other organisms. These results demonstrate that cells with a low content of polyQ or other aggregation-prone proteins can show a striking resilience with respect to polyQ toxicity and that genetic instability of repetitive DNA sequences may have played an important role in the evolutionary emergence and exclusion of polyQ expansion proteins in different organisms. IMPORTANCE Polyglutamine (polyQ) proteins encoded by repetitive CAG DNA sequences serve a variety of normal biological functions. Yet some proteins with abnormally expanded polyQ regions cause neurodegeneration through unknown mechanisms. To study how distinct cellular environments modulate polyQ aggregation and toxicity, we expressed CAG-expanded huntingtin fragments in Schizosaccharomyces pombe . In stark contrast to many other eukaryotes, S. pombe is uniquely devoid of proteins containing long polyQ tracts. Our results show that S. pombe cells, despite their low content of endogenous polyQ proteins, exhibit striking and unexpected resilience with respect to polyQ toxicity and that genetic instability of repetitive DNA sequences may have played an important role in the emergence and expansion of polyQ domains in eukaryotic evolution.

scholarly journals Computational Mining of Microsatellites in the Chloroplast Genome of Ptilidium pulcherrimum, a Liverwort

2014 ◽  
Vol 3 (3) ◽  
pp. 50-58
Author(s):  
Asheesh Shanker
Keyword(s):  
Chloroplast Genome ◽  
Dna Sequences ◽  
Pcr Primers ◽  
Repeat Type ◽  
Dinucleotide Repeats ◽  
Perl Script ◽  
Repeat Units ◽  
Chloroplast Genome Sequence ◽  
Nucleotide Repeats ◽  
Simple Sequence

Microsatellites also known as simple sequence repeats (SSRs) are found in DNA sequences. These repeats consist of short motifs of 1-6 bp and play important role in population genetics, phylogenetics and also in the development of molecular markers. In this study chloroplastic SSRs (cpSSRs) in the chloroplast genome of Ptilidium pulcherrimum, downloaded from the National Center for Biotechnology Information (NCBI), were detected. The chloroplast genome sequence of P. pulcherrimum was mined with the help of a Perl script named MISA. A total of 23 perfect cpSSRs were detected in 119.007 kb sequence mined showing density of 1 SSR/5.17 kb. Depending on the repeat units, the length of SSRs found to be 12 bp for mono and tri, 12 to “22 bp for di, 12 to 16 bp for tetra nucleotide repeats. Penta and hexanucleotide repeats were completely absent in chloroplast genome of P. pulcherrimum. Dinucleotide repeats were the most frequent repeat type (47.83%) followed by tri (21.74%) and tetranucleotide (21.74%) repeats. Out of 23 SSRs detected, PCR primers were successfully designed for 22 (95.65%) cpSSRs. DOI: http://dx.doi.org/10.3126/ije.v3i3.11063 International Journal of Environment Vol.3(3) 2014: 50-58

scholarly journals Novel repetitive sequences decipher the evolution and phylogeny in Carthamus L

2019 ◽  
Author(s):  
Shweta Mehrotra ◽  
Vinod Goyal
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Carthamus Tinctorius ◽  
Phylogeny Reconstruction ◽  
Reconstruction Method ◽  
Crop Species ◽  
Isolation And Characterization ◽  
Eukaryotic Genomes

Abstract Repetitive sequences are ubiquitous features of eukaryotic genomes, which contribute up to 70-80% of the nuclear genomic DNA. They are known to impact genome evolution and organization and play important role in genome remodelling. The widespread distribution and sufficient conservation of repeats reinforce the value of repetitive DNA sequences as markers of evolutionary processes. The repetitive DNA-based phylogeny reconstruction method is consistent in resolving expected phylogenetic and evolutionary relationships. In the present study, we address the isolation and characterization of four novel repetitive sequences (pCtHaeIII-I, pCtHaeIII-II, pCtHaeIII-III and pCtTaqI-I) from Carthamus tinctorius. Detailed phylogenetic analysis of 18 taxa belonging to 7 species of Carthamus has also been done with pCtHaeIII-I, and pCtHaeIII-II which clearly indicated concerted evolution while delineating phylogenetic relationships among the 18 taxa studied. The above understanding can assist in the marker assisted genetic improvement/ enhancement programmes in this crop species.

scholarly journals A CR1 element is embedded in a novel tandem repeat (HinfI repeat) within the chicken genome

Genome ◽  
2006 ◽  
Vol 49 (2) ◽  
pp. 97-103 ◽  
Author(s):  
Juan Li ◽  
Frederick C Leung
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Chicken Genome ◽  
Unique Region ◽  
Pericentric Region ◽  
Evolutionary Origins ◽  
Highly Repetitive Dna ◽  
Chicken Repeat ◽  
Eukaryotic Genomes

Highly repetitive DNA sequences constitute a significant portion of most eukaryotic genomes, raising questions about their evolutionary origins and amplification dynamics. In this study, a novel chicken repetitive DNA family, the HinfI repeat, was characterized. The basic repeating unit of this family displays a uniform length of 770 bp, which was defined by the recognition site of HinfI. The HinfI repeat was specifically localized in the pericentric region of chromosome 4 by fluorescence in situ hybridization and constitutes 0.51% of the chicken genome. Interestingly, a chicken repeat 1 (CR1) element has been identified within this basic repeating unit. Like other CR1 elements, this CR1 element also displays typical retrotransposition characteristics, including a highly conserved 3′ region and a badly truncated 5′ end. This direct evidence from sequence analysis, together with our Southern blot results, suggests that the HinfI repeat may originate from a unique region containing a retrotransposed CR1 element.Key words: satellite DNA, CR1 retrotransposon, HinfI repeat, Gallus gallus.

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