• Microsatellites are also known as simple sequence repeats (SSRs). (wikipedia.org)
  • The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. (researchgate.net)
  • In recent years, microsatellites, also known as simple sequence repeats (SSRs), have become the preferred type of marker. (usda.gov)
  • Microsatellites (Short sequence repeats, SSRs, Short tandem repeats): are short (1-6bp) repeating sequences in genetic code. (flashcardmachine.com)
  • BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)
  • Molecular markers such as single nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs) or microsatellites are used to genotype segregating populations. (bioline.com)
  • Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. (pacb.com)
  • We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. (pacb.com)
  • They are also known as short tandem repeats (STRs) or simple sequence repeats (SSRs). (vajiramandravi.com)
  • We observed 2 to 10 geographically segregated sequence types at each of 5 selected loci. (cdc.gov)
  • A neighbor-joining analysis was used to assess the genetic relatedness of various C. cayetanensis sequences for each locus and concatenated sequences of 5 loci. (cdc.gov)
  • Unique sequences generated from the 5 MLST loci were deposited in GenBank (accession nos. (cdc.gov)
  • These loci included 13 microsatellite and 2 minisatellite loci. (cdc.gov)
  • Phylogenetic relationships among sequence types of Cyclospora cayetanensis at 5 microsatellite loci: A) CYC3, B) CYC13, C) CYC15, D) CYC21, and E) CYC22. (cdc.gov)
  • accessions from Iran and the USA were characterized at 9 highly polymorphic microsatellite loci using fluorescent primers and a capillary electrophoresis fragment sizing system. (usda.gov)
  • 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)
  • 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)
  • The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. (datadryad.org)
  • Twenty one microsatellite loci were tested with eleven showing reliable amplification and polymorphism in K. senegalensis. (datadryad.org)
  • We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). (pacb.com)
  • To identify potential genotyping markers, we sequenced the genome of 1 C. cayetanensis isolate (CHN_HEN01) from Henan, China ( 3 ), and searched for microsatellite and minisatellite sequences among the first 40 of 4,811 assembled contigs by using Tandem Repeat Finder software ( http://tandem.bu.edu/trf/trf.html ). (cdc.gov)
  • Pseudomolecules as well as unmapped scaffolds were used for the bulk mining of SSR markers and for the construction of the first globe artichoke microsatellite marker database. (researchgate.net)
  • scolymus) has been used to catalog the genome's content of simple sequence repeat (SSR) markers. (researchgate.net)
  • Sixty-two types of grapes from Iran and the USA were characterized using nine previously identified microsatellite DNA markers. (usda.gov)
  • Here we describe the development of microsatellite markers for K. senegalensis using next generation sequencing in order to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. (datadryad.org)
  • Microsatellite markers are used for individual identification and, for paternity analysis in humans and animals. (genomia.cz)
  • In genetic diversity studies, the most frequently used markers are microsatellites. (intechopen.com)
  • To assess if the behavioral difference between the family and kenneled dogs could be due to genetic divergence of these two populations and/or to lower genetic diversity of the kenneled dogs, we analyzed their genetic structure using 11 microsatellite markers. (frontiersin.org)
  • We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers. (pacb.com)
  • This field of genetics emerged from the availability of several studies with classical molecular markers, such as isozymes, RAPD, AFLP, and microsatellites. (intechopen.com)
  • Microsatellite markers are very valuable in population genetics, conservation genetics, and phylogenetic research. (vajiramandravi.com)
  • microsatellite markers are available for the species (Bro wn et al. (researchgate.net)
  • To better understand the karyotype organization in Melipona and the relationship among the subgenera, we mapped repetitive sequences and analyzed previously reported cytogenetic data with the aim to identify cytogenetic markers to be used for investigating the phylogenetic relationships and chromosome evolution in the genus. (karger.com)
  • The aim of this Master thesis was to study the genetic diversity of alfalfa grown in Kyrgyzstan and in other countries and determine the genetic relationship using simple sequence repeat (SSR, microsatellite) molecular markers as well as to contribute to the development of synthetic alfalfa varieties for use as forage in Kyrgyzstan. (slu.se)
  • Microsatellite instability (MSI) is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR). (wikipedia.org)
  • Microsatellite instability structure consists of repeated nucleotides, most often seen as GT/CA repeats. (wikipedia.org)
  • Microsatellite instability (or MSI) is defined by the National Cancer Institute as a change that occurs in the DNA of certain cells, such as tumor cells, in which the number of repeats of microsatellites (short, repeated sequences of DNA) is different from the number of repeats that was in the DNA when it was inherited. (merck.com)
  • Low Levels of Microsatellite Instability at Simple Repeated Sequences Commonly Occur in Human. (iiarjournals.org)
  • Dr Marshall describes the impacts of microsatellite stability and instability on metastatic colorectal cancer. (ajmc.com)
  • Stage II patients with high microsatellite instability (MSI-H) have a better prognosis and do not benefit from 5-FU adjuvant treatment. (medscape.com)
  • The Web site "www.artichokegenome.unito.it" hosts all the available genomic sequences, together with their structural/functional annotations and project information are presented to users via the open-source tool JBrowse, allowing the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for Cynara cardunculus genomics. (researchgate.net)
  • In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
  • The past decade has seen a plethora of next-generation sequencing and data analysis studies, allowing us to map the genomic landscapes of various cancer types, while single cell analyses are shedding light on tumor heterogeneity. (iiarjournals.org)
  • Ultimately, the rapid development of sequencing technologies allowed studies at the genomic level, augmenting the resolution of association with environment factors. (intechopen.com)
  • An allele is one of two or more versions of DNA sequence (a single base or a segment of bases) at a given genomic location. (genome.gov)
  • Forty-three sequences containing simple sequence repeats or microsatellites were generated from an M13 library of total genomic mouse DNA. (ox.ac.uk)
  • Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
  • The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. (usgs.gov)
  • These isolates were previously typed by random amplified polymorphic DNA (RAPD), sequence-specific DNA polymorphism (SSDP), microsatellite polymorphism (MSP) and multilocus enzyme electrophoresis (MLEE). (elsevierpure.com)
  • The most common microsatellite in humans is a dinucleotide repeat of the nucleotides C and A, which occurs tens of thousands of times across the genome. (wikipedia.org)
  • The Emory researchers have found that the bonobo, an ape noted for its empathic traits, unlike its relative the chimpanzee, has a microsatellite with a sequence similar to that of humans. (news-medical.net)
  • Some research suggests that MSIs are short tandem DNA repeat sequences of one to six base pairs throughout the genome, while other research suggests that the range may be two to five. (wikipedia.org)
  • Although researchers do not agree on a specific threshold for the number of tandem repeats that constitute a microsatellite, there is a consensus around their relative size. (wikipedia.org)
  • These repeating units, which are typically 1-6 base pairs in length, are repeated in tandem, and the amount of repetitions varies between individuals. (vajiramandravi.com)
  • In the present study, 52 clinical isolates of A. fumigatus from 12 airway specimens from patients with invasive aspergillosis (hospitalized in three different centres) were characterized by short tandem repeat (STR) typing and multilocus sequence typing (MLST). (elsevierpure.com)
  • In this study, we developed a multilocus sequence typing (MLST) tool to help with identification of this protozoan. (cdc.gov)
  • The first stage involved identifying, in unrelated subjects showing linkage to 2q24-q33, genetic variants in exons and flanking sequence within candidate genes and comparing the frequency of the variants between autistic and unrelated nonautistic subjects. (neurotransmitter.net)
  • Using microsatellite analysis for loss of heterozygosity (LOH) at 11q13 and DNA sequencing of coding exons, the MEN1 gene was studied in 49 parathyroid lesions of patients with divergent symptoms, operative findings, histopathological diagnosis, and biochemical signs of nonfamilial pHPT. (lu.se)
  • Polymerase chain reaction-based assays can reveal these novel microsatellites and provide evidence for the presence of MSI. (wikipedia.org)
  • Size of a marker (number of base pair in a microsatellite) is detected by polymerase chain reaction (PCR) and subsequent fragment analysis. (genomia.cz)
  • These sequences were analyzed for size variation using the polymerase chain reaction and gel electrophoresis without the need for radiolabeling. (ox.ac.uk)
  • According to Young, far from being junk, the repetitive DNA sequences, which are highly prone to mutate rapidly, may ultimately exert their influence through complex interactions with other genes to produce individual differences and social diversity. (news-medical.net)
  • The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. (biomedcentral.com)
  • Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
  • Genetic mapping: Microsatellite DNA can be used to map the location of genes in the genome. (vajiramandravi.com)
  • Fragile X-Associated Tremor/Ataxia Syndrome (FXTAS) and Neuronal Intranuclear Inclusions Disease (NIID) are rare neurodegenerative disorders due to small expansions of GGC repeats located in the 5'UTR of the FMR1 and NOTCH2NLC genes, respectively. (igbmc.fr)
  • Although the length of microsatellites can vary from person to person and contributes to the individual DNA "fingerprint", each individual has microsatellites of a set length. (wikipedia.org)
  • DNA fingerprinting: Microsatellite DNA can be used to create a unique DNA fingerprint for an individual. (vajiramandravi.com)
  • A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genetic information encoding a particular amino acid. (genome.gov)
  • It is estimated that up to 40 to 50% of the human genome is composed of repeated DNA elements, among which microsatellites are short repeated sequences of 3 to 6 nucleotides. (igbmc.fr)
  • We designed primers for nested PCR analysis of the targets based on flanking nucleotide sequences. (cdc.gov)
  • We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
  • The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. (researchgate.net)
  • Bear researchers were at the forefront of using microsatellites to study the demographics and diversity of populations, such that 3 species have complete sampling and 3 others are represented across their range breadth. (bioone.org)
  • Yet there has not been a synthesis of these data within or among species because of difficulties comparing microsatellites. (bioone.org)
  • We extracted microsatellite summary statistics from 104 papers that sampled 284 populations of any species within Ursidae, then yardstick-transformed the data for direct comparison. (bioone.org)
  • The eleven novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. (datadryad.org)
  • The length of these repeating sequences , at one time dismissed as mere junk DNA, in the gene that codes for a key hormone receptor determined male-female relations and parenting behaviors in a species of voles. (news-medical.net)
  • for example, the repeating letter sequences are much longer in monogamous than in polygamous vole species, and even within a species, there are differences in the number of letters in the sequence among individuals. (news-medical.net)
  • Then they bred two strains of a monogamous species, the prairie vole, one with a long version of the microsatellites and the other with a short version. (news-medical.net)
  • With a growing understanding of the genetic sequences and make-up of selected species, a more targeted approach looks at total genomics - linking complex phenotypic traits to the genetic architecture and underlying molecular mechanisms to better instruct cross-breeding and back-breeding efforts. (bioline.com)
  • Researchers can analyse the genetic structure, population dynamics, and evolutionary relationships among various species of animals by analysing microsatellite DNA. (vajiramandravi.com)
  • The sequences obtained from each locus were aligned by using ClustalX version 2.1 ( http://www.clustal.org ). (cdc.gov)
  • However, 1-11 specimens did not produce readable sequences at each locus. (cdc.gov)
  • Nucleotide sequence alignment led to the identification of 4 sequence types at locus CYC3, 10 at locus CYC13, 2 at locus CYC15, 8 at locus CYC21, and 4 at locus CYC22 ( Technical Appendix Table 2). (cdc.gov)
  • The number of repeats at a certain microsatellite locus might vary greatly between people in a population because microsatellite DNA is highly variable. (vajiramandravi.com)
  • Microsatellite DNA is utilised in genetic analysis, more specifically in molecular genetics and genomics. (vajiramandravi.com)
  • Each newly sequenced genome contributes an average of 8,579 novel variants. (pacb.com)
  • The use by some variants of an alternate promoter in an upstream long terminal repeat (LTR) results in placenta-specific expression. (cancer-genetics.org)
  • The generation of a library of PCR-analyzed microsatellite variants for genetic mapping of the mouse genome. (ox.ac.uk)
  • Microsatellites were observed only in euchromatin regions, whereas the (TTAGG) 6 repeats were found at telomeric sites in both groups. (karger.com)
  • Population genetics: Microsatellite DNA can be used to study the genetic diversity of populations. (vajiramandravi.com)
  • In this paper, we present a significant improvement compared to Lander-Waterman's result and prove that by combining the sequencing and computing processes, one can re-sequence the whole genome with as low as O(G) sequenced bases in total. (pacb.com)
  • Data -- Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity. (datadryad.org)
  • Each offspring has to correspond with a parent in 50% of each microsatellite marker. (genomia.cz)
  • Microsatellite marker-based genetic diversity analysis and developing synthetic varieties in Alfalfa (Medicago sativa L. (slu.se)
  • Because the lack of typing tools for Cyclospora cayetanensis has hampered outbreak investigations, we sequenced its genome and developed a genotyping tool. (cdc.gov)
  • Longer sequences are called minisatellite, and even longer sequences are called satellite DNA sites. (wikipedia.org)
  • The majority of repeats occur in untranslated regions, specifically introns. (wikipedia.org)
  • Studies in our group are focused on how microsatellite expansions located in the "non-coding" parts (5'UTR, Introns, 3'UTR, etc.) of the human genome cause genetic diseases. (igbmc.fr)
  • It can be tested by immunohistochemistry, next-generation sequencing, and fragment analyses. (ajmc.com)
  • The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)
  • In 1991, I went on postdoc to Mark Chase's lab in Chapel Hill, NC to learn more about the systematics of the Acanthaceae by using restriction site mapping and gene sequencing. (lu.se)
  • Next generation sequencing yielded 93 943 sequences with an average read length of 234 bp. (datadryad.org)
  • With ongoing advances and applications of next generation sequencing (NGS), an understanding of the genetic diversity within breeding material is increasing at a rapid pace, helping to improve knowledge of so-called 'orphan' crops and integrate the various core components of molecular breeding programs. (bioline.com)
  • Next-generation sequencing (NGS) technologies revolutionized assessing viral genetic diversity experimentally. (pacb.com)
  • Diagnostic Yield of a Targeted Next-Generation Sequencing Gene Panel for Pediatric-Onset Movement Disorders: A 3-Year Cohort Study. (cdc.gov)
  • Targeted broad-based genetic testing by next-generation sequencing informs diagnosis and facilitates management in patients with kidney diseases. (cdc.gov)
  • Microsatellites make up approximately three percent of the human genome, or more than one million fragments of DNA. (wikipedia.org)
  • See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
  • We find that 84% of an individual human genome can be sequenced confidently. (pacb.com)
  • While all researchers agree that microsatellites are repeat sequences, the lengths of the sequences remain in question. (wikipedia.org)
  • The researchers first demonstrated in cell cultures that the vole vasopressin receptor microsatellites could modify gene expression. (news-medical.net)
  • The researchers suggest that variability in vasopressin receptor microsatellite length could help account for differences in normal human personality traits, such as shyness, and perhaps influence disorders of sociability like autism and social anxiety disorders. (news-medical.net)
  • The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century. (pacb.com)
  • Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. (pacb.com)
  • Perfect repeats mutate about 2 × more often than imperfect repeats. (biomedcentral.com)
  • However, microsatellites that occur in coding regions often inhibit the expansion of most downstream events. (wikipedia.org)
  • Variations of DNA microsatellites size and sequence occur naturally and have important roles in genome evolution. (igbmc.fr)
  • This method can generate tens of billions of copies of a particular DNA fragment (the sequence of interest, DNA of interest, or target DNA) from a DNA extract (DNA template). (intechopen.com)
  • These sequences can be made of units of 1 to 6 base pairs in length that are repeated and reside adjacent to each other in the genome. (wikipedia.org)
  • Some scientists distinguish among the three categories by a minimum number of base pairs, and others use a minimum number of repeated units. (wikipedia.org)
  • These microsatellites contain sequences repeated in tandems from two to seven base pairs. (genomia.cz)
  • The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)
  • Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)
  • As of 2003, 99% of the chemical base pairs that make up human DNA had been sequenced to within 99.99% accuracy. (medscape.com)
  • Indeed, if the sequence of interest is present in the DNA extract, it is possible to selectively replicate it (we speak of amplification) in very large numbers. (intechopen.com)
  • The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. (researchgate.net)
  • However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. (biomedcentral.com)
  • If [they're] microsatellite instable, then do genetic analysis to confirm and make sure you do germline testing to see if the patient is has Lynch syndrome. (ajmc.com)
  • With advances in library preparation, increasing sensitivity of sequencing platforms, and more sophisticated models, it might be possible to detect all or most viral strains in a single individual. (pacb.com)
  • However, variation in microsatellite size is also the source of devastating disorders, as more than 40 inherited developmental, neuromuscular and neurodegenerative human genetic diseases are caused by microsatellite expansions. (igbmc.fr)
  • Microsatellites are causative agents in a variety of diseases. (flashcardmachine.com)
  • These CTG and CCTG repeats are transcribed into mutant CUG or CCUG RNA that bind and sequester the MBNL RNA binding proteins, resulting in specific RNA metabolism changes that cause the neuromuscular symptoms of these diseases. (igbmc.fr)
  • This high-confidence region includes 91.5% of exon sequence and 95.2% of known pathogenic variant positions. (pacb.com)
  • An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)
  • Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc. (usgs.gov)
  • A database, called "Cynara cardunculus MicroSatellite DataBase" (CyMSatDB) was developed to provide a searchable interface to the SSR data. (researchgate.net)
  • SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. (usgs.gov)
  • The rbcL sequence data we produced was combined with rbcL sequences from many other labs, and in 1993 we published the first comprehensive paper describing the phylogeny of Flowering plants based on gene sequences. (lu.se)