The rDNA repeats have many regulatory mechanisms that keep the DNA from undergoing mutations, thus keeping the rDNA conserved. (wikipedia.org)
Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. (biomedcentral.com)
To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. (biomedcentral.com)
It is possible that each of these mechanisms contributes to the high mutation rate of STRs, but strand slippage is the mechanism proposed for generating most observed mutations in STR loci [ 19 ]. (biomedcentral.com)
Therefore, we investigated the 17 Yfiler Y-STRs in 1,730-1,764 DNA-confirmed father-son pairs per locus and found 84 sequence-confirmed mutations among the 29,792 meiotic transfers covered. (springer.com)
Of the 84 mutations, 83 (98.8%) were single-repeat changes and one (1.2%) was a double-repeat change (ratio, 1:0.01), as well as 43 (51.2%) were repeat gains and 41 (48.8%) repeat losses (ratio, 1:0.95). (springer.com)
Our finding of three Y-STR mutations in one father-son pair (and two pairs with two mutations each) has consequences for determining the threshold of allelic differences to conclude exclusion constellations in future applications of Y-STRs in paternity testing and pedigree analyses. (springer.com)
Replication1
They could occur by slippage of the newly synthesized strand during DNA replication or by gene conversion. (wikipedia.org)
Nucleotide1
The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. (ijpsr.com)
Genomes1
of tandem repeats within their genomes [6, 17]. (scirp.org)
Polymorphisms4
In the large rDNA array, polymorphisms between rDNA repeat units are very low, indicating that rDNA tandem arrays are evolving through concerted evolution. (wikipedia.org)
However, the mechanism of concerted evolution is imperfect, such that polymorphisms between repeats within an individual can occur at significant levels and may confound phylogenetic analyses for closely related organisms. (wikipedia.org)
The Y-chromosomal short tandem repeat (Y-STR) polymorphisms included in the AmpF l STR® Yfiler® polymerase chain reaction amplification kit have become widely used for forensic and evolutionary applications where a reliable knowledge on mutation properties is necessary for correct data interpretation. (springer.com)
A reliable knowledge of the particular Y-chromosomal short tandem repeat (Y-STR) polymorphisms used in the forensic context is essential for the correct interpretation of the resulting profiles. (springer.com)
Imperfect1
Perfect repeats mutate about 2 × more often than imperfect repeats. (biomedcentral.com)
Repetitive DNA1
We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. (elifesciences.org)
Evolutionary1
The different coding regions of the rDNA repeats usually show distinct evolutionary rates. (wikipedia.org)
Mutation1
In forensics, mutation rates are needed when STRs are applied to paternity testing, and Y-STRs are especially powerful in deficiency cases of disputed paternity involving male offspring where the alleged father is not available for DNA analysis but is replaced by any of his male paternal relatives. (springer.com)
Loci2
Due to the repetitive structure of STRs and their high mutability, sequencing and genotyping these loci is difficult, especially using short-read sequencing data. (biomedcentral.com)
Some of these tools are designed to detect STR expansions at disease-related loci, while others detect expansions and contractions of STRs genome-wide but are constrained by sequencing read length and the STR motif size. (biomedcentral.com)
Amplification1
These sequences regulate transcription initiation and amplification, and contain both transcribed and non-transcribed spacer segments. (wikipedia.org)
Mechanisms1
Mechanisms by which E. chaffeensis establishes intracellular infection, and avoids host defenses are not well understood, but involve functionally relevant host-pathogen interactions associated with tandem and ankyrin repeat effector proteins. (frontiersin.org)
Species5
the result revealed that insertions and deletions occurred frequently between species and often flanked by conserved sequences. (wikipedia.org)
Between remote species as human and frog comparison of sequences at ITS tracts is not appropriate. (wikipedia.org)
Conserved sequences at coding regions of rDNA allow comparisons of remote species, even between yeast and human. (wikipedia.org)
In cases for sibling species, comparison of the rDNA segment including ITS tracts among species and phylogenetic analysis are made satisfactorily. (wikipedia.org)
We report our analysis of MyoD1 and MyoD2 protein sequences from 54 teleost species, and show that O. alcalica , along with some other teleosts, include a polyserine repeat between the amino terminal transactivation domains (TAD) and the cysteine-histidine rich region (H/C) in MyoD1. (mdpi.com)
Short1
Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
Present1
5S rDNA is also present in independent tandem repeats as in Drosophila. (wikipedia.org)
Found1
The rRNA transcribed from the approximately 600 rDNA repeats forms the most abundant section of RNA found in cells of eukaryotes. (wikipedia.org)
Units1
The rRNA transcriptional units are clustered in tandem repeats. (wikipedia.org)
Damage1
Also, any damage or disruption to the enzymes that protect the tandem repeats of the rDNA, can result in lower synthesis of ribosomes, which also lead to other defects in the cell. (wikipedia.org)
Study1
In our study, online resources for comparative genomics analysis between strains by using databases such as MGDD (Mycobacterial Genome Divergence Database), Biohealth base, GenomycDB, Mycobacterium tuberculosis database, and TBDB (Tuberculosis Database). (ijpsr.com)
Repetitive4
Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. (plos.org)
Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. (plos.org)
Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. (plos.org)
We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile . (biomedcentral.com)
Genomic2
In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. (plos.org)
This review on eucalypts microsatellites, highlights the availability and characteristics of genomic and eSSRs and their potential in genetic analysis of natural and breeding populations and also discusses the future prospects in population genetics and marker assisted selection. (springeropen.com)
19961
One of the most frequently used DNA markers in eucalypts since 1996 are microsatellites or simple sequence repeats (SSRs) (Byrne et al. (springeropen.com)
Phylogenetic3
However, the mechanism of concerted evolution is imperfect, such that polymorphisms between repeats within an individual can occur at significant levels and may confound phylogenetic analyses for closely related organisms. (wikipedia.org)
In cases for sibling species, comparison of the rDNA segment including ITS tracts among species and phylogenetic analysis are made satisfactorily. (wikipedia.org)
Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. (biomedcentral.com)
Genome4
Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. (plos.org)
Whole genome sequence and expressed sequence tags (ESTs) of the eucalypts paved way for introduction of molecular genetics and breeding in this genus. (springeropen.com)
The importance of microsatellites for plant genome analysis has been highlighted on several occasions (Varshney et al. (springeropen.com)
Subsequently, development of online databases like GenBank led to the generation of Expressed Sequence Tag (EST) derived-SSRs (eSSRs) which are present in transcribed regions of the genome. (springeropen.com)
Newly1
They could occur by slippage of the newly synthesized strand during DNA replication or by gene conversion. (wikipedia.org)
Mechanism1
Transition from pre- to full mutation requires large gains in size, usually from about 100 to more than 1000 triplets, which cannot be created by a simple polymerase slippage mechanism. (bmj.com)
SSRs3
a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. (biomedcentral.com)
Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F 2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. (biomedcentral.com)
Different molecular characterization approaches have been used simultaneously in eucalypts, however, microsatellites or simple sequence repeats (SSRs) with their prolific characteristics could occupy a special niche in Eucalyptus genetic improvement. (springeropen.com)
Clonal1
Increase of FMRP expression, raised levels ofFMR1 mRNA, and clonal selection in proliferating cells with unmethylated fragile X repeat expansions: a clue to the sex bias in the transmission of full mutations? (bmj.com)
Genetic1
Efforts on molecular breeding and molecular genetic analysis are underway in eucalypts to accelerate breeding and conservation. (springeropen.com)
Variation1
We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. (biomedcentral.com)
Individual2
Increased ploidy level and individual repeats in high copy number are common in angiosperms but are rarely seen in gymnosperms [4] , [5] . (plos.org)
9 10 By lateral spreading, each individual CpG dinucleotide may be involved 11-13 particularly in the CGG repeat and the FMR1 promoter. (bmj.com)
Made2
Recent advances in the cost and utility of second generation, high-throughput sequencing technologies have made it possible for ten conifer reference genomes to be assembled ( http://www.pinegenome.org/pinerefseq ). (plos.org)
However, in recent times, tremendous data on gSSRs and eSSRs are made available through next generation sequencing (NGS) methods (Zalapa et al. (springeropen.com)
Regions1
Conserved sequences at coding regions of rDNA allow comparisons of remote species, even between yeast and human. (wikipedia.org)
Long1
GAGs are long, linear polysaccharide molecules composed of repeating dimers, each of which contains a hexuronic acid (or galactose in the case of keratan sulfate) and an amino sugar. (medscape.com)
Comparison1
Between remote species as human and frog comparison of sequences at ITS tracts is not appropriate. (wikipedia.org)
Databases2
DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. (biomedcentral.com)
Typing procedures based on DNA sequences overcome these limitations, since sequence data may easily be exchanged and stored in databases that are accessible via the internet. (biomedcentral.com)
Data1
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
Efforts1
Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. (plos.org)
Full2
In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. (plos.org)
1-3 Disease alleles, containing more than 220 CGG triplets and designated full mutations, only arise upon transmission from a mother who carries a premutation allele that is characterised by repeat sizes between 60 and 200 and is not associated with intellectual deficits. (bmj.com)