Journal articles on the topic 'Microsatellites'
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1
Basharat, Zarrin, and Azra Yasmin. "Survey of compound microsatellites in multiple Lactobacillus genomes." Canadian Journal of Microbiology 61, no. 12 (December 2015): 898–902. http://dx.doi.org/10.1139/cjm-2015-0136.
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Distinct simple sequence repeats with 2 or more individual microsatellites joined together or lying adjacent to each other are identified as compound microsatellites. Investigation of such composite microsatellites in the genomes of genus Lactobacillus was the aim of this study. In silico inspection of microsatellite clustering in genomes of 14 Lactobacillus species revealed a wealth of compound microsatellites. All of the mined compound microsatellites were imperfect, were composed of variant motifs, and increased in all genomes, with maximum distance (dMAX) increments of 10 to 50. The majority of these repeats were present in the coding regions. A correlation of microsatellite to compound microsatellite density was detected. The difference established in compound microsatellite division among eukaryotes, Escherichia coli, and lactobacilli is suggestive of diverse genomic features and elementary distinction between creation and fixation methods of compound microsatellites among these organisms.
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Harker, N., L. R. Rampling, M. R. Shariflou, M. J. Hayden, T. A. Holton, M. K. Morell, P. J. Sharp, R. J. Henry, and K. J. Edwards. "Microsatellites as markers for Australian wheat improvement." Australian Journal of Agricultural Research 52, no. 12 (2001): 1121. http://dx.doi.org/10.1071/ar01025.
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Microsatellite markers have been shown to be highly polymorphic and simple to use in hexaploid wheat. This study aimed to establish microsatellites as informative markers for Australian wheat improvement. By screening microsatellites developed as part of the Wheat Microsatellite Consortium and other available microsatellite sources, 257 informative microsatellites for Australian wheat varieties were identified and reported in the Australian National Wheat Molecular Marker Program microsatellite database (http://www.scu.edu.au/research/cpcg/). Of these, 151 microsatellites identifying 172 loci were scored on at least 1 of 4 double haploid mapping populations and were then integrated, where possible, into existing genetic maps. Polymorphism information content values were calculated for most microsatellites to establish a reference for their value for future investigations. The mapping of available microsatellites enhances the quality of the genetic maps and may provide useful genetic markers for traits of interest to the Australian wheat breeding programs.
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Yu, Kangfu, Soon J. Park, and Vaino Poysa. "Abundance and variation of microsatellite DNA sequences in beans (Phaseolus andVigna)." Genome 42, no. 1 (February 1, 1999): 27–34. http://dx.doi.org/10.1139/g98-100.
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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.
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England, Phillip R., David A. Briscoe, and Richard Frankham. "Microsatellite polymorphisms in a wild population of Drosophila melanogaster." Genetical Research 67, no. 3 (June 1996): 285–90. http://dx.doi.org/10.1017/s0016672300033760.
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SummaryHighly variable DNA polymorphisms called microsatellites are rapidly becoming the marker of choice in population genetic studies. Until now, microsatellites have not been utilized for Drosophila studies. We have identified eight polymorphic microsatellite loci in Drosophila melanogaster and used them to characterize the genetic variation in a wild population from the Tyrrell's winery in Australia. Microsatellites were isolated from a partial genomic DNA library. All microsatellites consist of (AC)n repeats ranging from n = 2 to n = 24. Six loci were assigned to chromosomal location by genetic mapping, with three loci on chromosome II, one locus on chromosome III and two loci on the X chromosome. Up to four microsatellite loci were multiplexed in the same reaction. Microsatellite variation is substantially greater than allozyme variation in the Tyrrell's Drosophila population. 80% of the microsatellite loci examined are polymorphic, compared with 28% of allozymes. The mean number of alleles per polymorphic locus is 5·2 in microsatellites compared with 30 in allozymes. The average observed heterozygosity of polymorphic microsatellites is 47% compared with 26% for allozymes. Microsatellite variation in Drosophila melanogaster is similar to that reported for other insects. Higher variability commends microsatellites over allozymes for genetic studies in Drosophila melanogaster.
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Xu, Zhenkang, Laura Gutierrez, Matthew Hitchens, Steve Scherer, Amy K. Sater, and Dan E. Wells. "Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis." Bioinformatics and Biology Insights 2 (January 2008): BBI.S561. http://dx.doi.org/10.4137/bbi.s561.
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The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.
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Areshchenkova, Tatyana, and Martin W. Ganal. "Long tomato microsatellites are predominantly associated with centromeric regions." Genome 42, no. 3 (June 1, 1999): 536–44. http://dx.doi.org/10.1139/g98-155.
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Microsatellites as genetic markers are used in many crop plants. Major criteria for their usability as molecular markers include that they are highly polymorphic and evenly spread throughout a genome. In tomato, it has been reported that long arrays of tetranucleotide microsatellites containing the motif GATA are highly clustered around the centromeres of all chromosomes. In this study, we have isolated tomato microsatellites containing long arrays (> 20 repeats) of the dinucleotide motifs GA, GT, AT, as well as GATA, assessed their variability within Lycopersicon esculentum varieties and mapped them onto a genetic map of tomato. The investigated microsatellite markers exhibited between 1 and 5 alleles in a diverse set of L. esculentum lines. Mapping of the microsatellites onto the genetic map of tomato demonstrates that, as previously shown, GATA microsatellites are highly clustered in the regions of the tomato centromeres. Interestingly, the same centromeric location was now found for long dinucleotide microsatellite markers. Because of this uneven distribution, genetic mapping of the entire tomato genome using long dinucleotide microsatellites will be very difficult to achieve and microsatellite markers with shorter arrays of microsatellites could be more suitable for mapping experiments albeit their lower level of polymorphism. Some microsatellite markers described in this study might provide a useful tool to study the molecular structure of tomato centromeric regions and for variety identification.Key words: molecular marker, Lycopersicon esculentum, genetic variability, genetic map, simple sequence repeats.
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Buschiazzo, E., and N. J. Gemmell. "Evolutionary and phylogenetic significance of platypus microsatellites conserved in mammalian and other vertebrate genomes." Australian Journal of Zoology 57, no. 4 (2009): 175. http://dx.doi.org/10.1071/zo09038.
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Building on the recent publication of the first monotreme genome, that of the platypus, and the discovery that many platypus microsatellites are found in the genomes of three mammals (opossum, human, mouse) and two non-mammalian vertebrates (chicken, lizard), we investigated further the evolutionary conservation of microsatellites identified in the monotreme lineage and tested whether the conservation of microsatellites we observe in vertebrates has phylogenetic signal. Most conserved platypus microsatellites (75%) were found in one species, with the platypus sharing many more microsatellites with mammals than with reptiles (83% versus 30%). Within mammals, unexpectedly, many more platypus microsatellites had orthologues in the opossum genome than in that of either human or mouse, which was at odds with the very well supported view that monotremes diverged from a lineage containing both eutherians and marsupials (Theria hypothesis). We investigated the phylogenetic significance of microsatellite conservation through Bayesian and maximum parsimony tree reconstruction using presence/absence data of microsatellite loci conserved in a total of 18 species, including the platypus. Although models of evolution implemented in current phylogenetic reconstruction algorithms are not tailor-made for microsatellite data, we were able to construct vertebrate phylogenies that correspond well to the accepted mammalian phylogeny, with two of our three reconstructions supporting the Theria hypothesis. Our analysis provides ground for new theoretical development in phylogeny-based analyses of conserved microsatellite data.
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Kaur, Simerpreet. "Microsatellite diversity in four cultivated species of Actinidiaceae and Rutaceae." Bioinformation 19, no. 3 (March 31, 2023): 230–34. http://dx.doi.org/10.6026/97320630019230.
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Microsatellites or Simple Sequence Repeats (SSRs) are short iterations of 1-6 bp in the genomes of almost all living organisms. Our study aimed to explore the microsatellite diversity in four cultivated species, namely Actinidia chinensis, Actinidia eriantha, Citrus maxima, and Citrus sinensis of the Actinidiaceae and Rutaceae families. We present a comprehensive analysis of microsatellite abundance, distribution, and motif composition in the genomes of these species. The association of microsatellite abundance with genomic features such as genome size, GC content, number of microsatellites, relative abundance, and relative density was also examined. The results revealed significant variations in the frequency and distribution of microsatellites across the genomes of these four species. Notably, a positive correlation was observed between genome size and microsatellite number as well as with GC content, indicating that larger genomes provide more opportunities for the accumulation of microsatellites. Furthermore, a negative correlation of genome size with relative microsatellite abundance and relative density was observed. These findings provide new insights into the microsatellite landscape of Actinidiaceae and Rutaceae, which could be explored for the development of microsatellite markers for diverse applications in the characterization of genetic diversity, molecular plant breeding, and phylogenetic analysis.
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He, Yu, Hongmei Li, Derek Brown, Franco Lamberti, and Maurice Moens. "Isolation and characterisation of microsatellites for Xiphinema index using degenerate oligonucleotide primed PCR." Nematology 5, no. 6 (2003): 809–19. http://dx.doi.org/10.1163/156854103773040718.
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Abstract A short insert genomic library for Xiphinema index, the natural vector of Grapevine Fanleaf Virus, was constructed from degenerate oligonucleotide primed PCR (DOP-PCR) products. The genomic library was screened for (CA)n microsatellites. Screening of 6200 colonies and comparison of the sequencing results revealed seven (CA)n containing microsatellites, coded here as XIMSL1, XIMSL2, XIMSL3, XIMSL4, XIMSL5, XIMSL6 and XIMSS1. XIMSL prefixed microsatellites were followed by the motif of the same long interspersed element. Microsatellite XIMSS1 has some similarity to the short interspersed element. Except for XIMSL1, all microsatellites were proven to be effective diagnostic tools at species level. Genetic diversity between and within populations was also evaluated for each microsatellite.
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Brooker, Amanda L., Doug Cook, Paul Bentzen, Jonathan M. Wright, and Roger W. Doyle. "Organization of Microsatellites Differs between Mammals and Cold-water Teleost Fishes." Canadian Journal of Fisheries and Aquatic Sciences 51, no. 9 (September 1, 1994): 1959–66. http://dx.doi.org/10.1139/f94-198.
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Microsatellites, in particular (dG-dT)n and (dG-dA)n dinucleotide repeats, are abundant and display a high degree of length polymorphism and heterozygosity in eukaryotic genomes. Here, we report the cloning and characterization of 64 microsatellite sequences from Atlantic cod, Gadus morhua. The microsatellites were classified as perfect, imperfect, and compound repeats. The length and integrity of these repeats were compared with microsatellites characterized from two other teleosts, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar), and from three mammalian genomes, human, porcine, and canine. Differences were found in the proportions of the repeat classes; however, the most significant difference between microsatellites from teleost fishes and mammals was the propensity of the former to be of greater length: some cod and rainbow trout microsatellites were more than twice the size of the longest microsatellite repeats reported for any mammalian genome. Primers for PCR amplification were constructed for seven of the cod microsatellites. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for a sample population. Amplification with these cod primers was also carried out on a number of related gadids. These polymorphic microsatellite loci have enormous potential utility as genetic markers for use in population, breeding, and evolutionary studies.
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Kaundun, Shiv Shankhar, and Satoru Matsumoto. "Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis." Genome 45, no. 6 (December 1, 2002): 1041–48. http://dx.doi.org/10.1139/g02-070.
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The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species. Key words: tea, Camellia sinensis, SSR, microsatellites, genetic diversity.
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Harr, Bettina, and Christian Schlötterer. "Long Microsatellite Alleles in Drosophila melanogaster Have a Downward Mutation Bias and Short Persistence Times, Which Cause Their Genome-Wide Underrepresentation." Genetics 155, no. 3 (July 1, 2000): 1213–20. http://dx.doi.org/10.1093/genetics/155.3.1213.
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Abstract Microsatellites are short tandemly repeated DNA sequence motifs that are highly variable in most organisms. In contrast to mammals, long microsatellites (>15 repeats) are extremely rare in the Drosophila melanogaster genome. To investigate this paucity of long microsatellites in Drosophila, we studied 19 loci with exceptionally long microsatellite alleles. Inter- and intraspecific analysis showed that long microsatellite alleles arose in D. melanogaster only very recently. This lack of old alleles with many repeats indicated that long microsatellite alleles have short persistence times. The size distribution of microsatellite mutations in mutation-accumulation lines suggests that long alleles have a mutation bias toward a reduction in the number of repeat units. This bias causes the short persistence times of long microsatellite alleles. We propose that species-specific, size-dependent mutation spectra of microsatellite alleles may provide a general mechanism to account for the observed differences in microsatellite length between species.
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Anand, Khushbu, Sonu Kumar, Afroz Alam, and Asheesh Shankar. "Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)." Plant Science Today 6, sp1 (December 31, 2019): 635–38. http://dx.doi.org/10.14719/pst.2019.6.sp1.697.
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Microsatellites or SSRs are the markers of selection due to their reproducibility, degree of polymorphism, distribution throughout the genome and co-dominant nature. Microsatellites are used primarily to study the genetic variability in various species and marker aided selection. Since microsatellites can be readily amplified by PCR, they have been utilized most extensively. To reduce time and cost to a great extent, the computational approach for identifying and developing microsatellite markers by mining nucleotide sequences is preferred over the conventional methods. In the present analysis, an in-silico method was used to detect microsatellites effectively in mitochondrial genomes of Anomodon rugelii (Müll. Hal.) Keissl., Anomodon attenuatus (Hedw.) Hueb., Climacium americanum (Renauld & Cardot) Kindberg, and Hypnum imponens Hedw. (Bryopsida; Hypnales). A total of 101 perfect microsatellites were mined with an average density of 1 microsatellite/4.21 kb. The hexa-nucleotide repeats were not detected in mitochondrial genomes of studied taxa. Di-nucleotides were seen to be the most frequent repeats followed by tetra-nucleotides. The identified microsatellites were also checked for variability in length between species. The mined microsatellites will be used for gene tagging, species identification and population genetic studies.
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Ma, Z. Q., M. Röder, and M. E. Sorrells. "Frequencies and sequence characteristics of di-, tri-, and tetra-nucleotide microsatellites in wheat." Genome 39, no. 1 (February 1, 1996): 123–30. http://dx.doi.org/10.1139/g96-017.
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Microsatellites have emerged as an important source of genetic markers for eukaryotic genomes. In this report, two wheat (Triticum aestivum L.) genomic libraries were screened for several di-, tri-, and tetra-nucleotide tandem repeats. Clones containing (AC)n, (AG)n, (TCT)n, and (TTG)n repeats were isolated and sequenced. On average, there was one (AC)n microsatellite every 292 kbp and one (AG)n microsatellite every 212 kbp. The trinucleotide tandem repeats (TCT)n and (TTG)n were about 10 times less common than the two dinucleotide tandem repeats tested and tetranucleotide tandem repeats were rare. Many of the microsatellites had more than 10 repeats. The maximum repeat number found for (AC)n was 36 and for (TCT)n was more than 50. The prevailing category of (AG)n microsatellites from (AG)n isolates was perfect repeats. About half of the (AC)n microsatellites were compound repeats, while most of the (TCT)n microsatellites were imperfect repeats. In a small sample, (TTG)n microsatellites consisted mainly of compound repeats. The most frequently associated repeats were (AC)n with (AG)n, (TCT)n with (TCC)n, and (TTG)n with (TGG)n. Among 32 pairs of microsatellite primers surveyed, seven produced polymorphic products in the expected size range and these loci were mapped using a hexaploid wheat mapping population or aneuploid stocks. Key words : wheat, Triticum aestivum L., microsatellites, polymorphism, sequence characteristics.
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Hale, M. L., A. M. Borland, and K. Wolff. "High degree of conservation of nuclear microsatellite loci in the genus Clusia." Genome 48, no. 5 (October 1, 2005): 946–50. http://dx.doi.org/10.1139/g05-048.
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In plants, microsatellites and their flanking DNA are rarely conserved across a whole genus, let alone other genera in the same family. Therefore, the possibility of using microsatellite primers developed for a species across a large number of plant species in the same genus is often limited. Remarkably, dinucleotide nuclear microsatellites developed for Clusia minor and for Clusia nemorosa amplified homologous microsatellites in species across the whole genus Clusia. In this present study, we report on the DNA sequence variation across the genus of 3 microsatellite loci with varying levels of variation. Compared over the species, there was a correlation between the lengths of the microsatellite loci. Interrupts occurred multiple times and did not seem to lead to the death of the microsatellite. These highly conserved markers will be useful for studying the variable reproductive systems in the genus Clusia.Key words: microsatellite, Clusia, cross-species amplification, microsatellite evolution.
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WILDER, J. A., T. DIAZ, R. J. W. O'NEILL, J. KENNEY, and H. HOLLOCHER. "Characterization and isolation of novel microsatellites from the Drosophila dunni subgroup." Genetical Research 80, no. 3 (December 2002): 177–85. http://dx.doi.org/10.1017/s0016672302005864.
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We have isolated and characterized 77 novel microsatellites from two species, Drosophila dunni and Drosophila nigrodunni, which are closely related Caribbean-island endemics from the Drosophila cardini species group. These species are very distantly related to all other Drosophila from which microsatellites have previously been characterized. We find that the average length of microsatellites isolated in these species is quite small, with an overall mean length of 9·8 repeat units for dinucleotide microsatellites in the two study species. The nucleotide composition of dinucleotides differs between the two species: D. nigrodunni has a predominance of (AC/GT)n repeats, whereas D. dunni has equal numbers of (AC/GT)n and (AG/CT)n repeats. Tri- and tetranucleotide repeats are not abundant in either species. We assayed the variability of eight microsatellites in a closely related third species, Drosophila arawakana, using wild-caught individuals from the island of Guadeloupe. We found the microsatellites to be extremely variable in this population, with observed heterozygosities ranging from 0·541 to 0·889. DNA amplification trials suggest that these eight microsatellites are widely conserved across the D. cardini group, with five of the eight producing amplification products in every species tested. However, the loci are very poorly conserved over greater phylogenetic distances. DNA amplification of the microsatellite loci was unreliable in members of the closely related Drosophila quinaria, Drosophila calloptera, Drosophila guarani and Drosophila tripunctata species groups. Furthermore, these microsatellites could not be detected in the genome of Drosophila melanogaster, despite the conservation of microsatellite flanking regions at some loci. These data indicate that Drosophila microsatellite loci are quite short lived over evolutionary timescales relative to many other taxa.
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Masuzaki, Shinichi, Naoyuki Araki, Naoki Yamauchi, Naoko Yamane, Tadayuki Wako, Akio Kojima, and Masayoshi Shigyo. "Chromosomal Locations of Microsatellites in Onion." HortScience 41, no. 2 (April 2006): 315–18. http://dx.doi.org/10.21273/hortsci.41.2.315.
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Bulb onion (Allium cepa L.) has a very large genome composed of a high proportion of repetitive DNAs. Genetic analyses of repetitive sequences may reveal microsatellites in order to increase the number of genetic markers in onion. Thirty microsatellites were previously isolated from an onion genomic library (Fischer and Bachmann, 2000). A complete set of Japanese bunching onion (A. fistulosum) – shallot (A. cepa Aggregatum group) monosomic addition lines were used to assign these microsatellites to the chromosomes of A. cepa. Simplified PCR conditions for each microsatellite were determined and 28 of the 30 primer pairs amplified DNA fragments, of which 21 microsatellite markers were assigned to chromosomes of A. cepa. Subsequent mapping of these microsatellites will enable us to establish the chromosomal distribution of these markers.
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Zhou, Y., T. Bui, L. D. Auckland, and C. G. Williams. "Undermethylated DNA as a source of microsatellites from a conifer genome." Genome 45, no. 1 (February 1, 2002): 91–99. http://dx.doi.org/10.1139/g01-119.
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Developing microsatellites from the large, highly duplicated conifer genome requires special tools. To improve the efficiency of developing Pinus taeda L. microsatellites, undermethylated (UM) DNA fragments were used to construct a microsatellite-enriched copy library. A methylation-sensitive restriction enzyme, McrBC, was used to enrich for UM DNA before library construction. Digested DNA fragments larger than 9 kb were then excised and digested with RsaI and used to construct nine dinucleotide and trinucleotide libraries. A total of 1016 microsatellite-positive clones were detected among 11 904 clones and 620 of these were unique. Of 245 primer sets that produced a PCR product, 113 could be developed as UM microsatellite markers and 70 were polymorphic. Inheritance and marker informativeness were tested for a random sample of 36 polymorphic markers using a three-generation outbred pedigree. Thirty-one microsatellites (86%) had single-locus inheritance despite the highly duplicated nature of the P. taeda genome. Nineteen UM microsatellites had highly informative intercross mating type configurations. Allele number and frequency were estimated for eleven UM microsatellites using a population survey. Allele numbers for these UM microsatellites ranged from 3 to 12 with an average of 5.7 alleles/locus. Frequencies for the 63 alleles were mostly in the lowcommon range; only 14 of the 63 were in the rare allele (q < 0.05) class. Enriching for UM DNA was an efficient method for developing polymorphic microsatellites from a large plant genome.Key words: hypomethylation, simple-sequence repeats, repetitive DNA, Pinus taeda L., gymnosperms.
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Azmir, I. A., I. S. Md-Yasin, and Y. Esa. "Microsatellite Marker Mining Using PCR-Based Isolation of Microsatellite Arrays (PIMA) Method on Blue-Spotted Mudskipper, Boleophthalmus Boddarti." IOP Conference Series: Earth and Environmental Science 995, no. 1 (April 1, 2022): 012051. http://dx.doi.org/10.1088/1755-1315/995/1/012051.
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Abstract Microsatellites are small and are codominant markers that can be amplified with polymerase chain reaction. Both prokaryotic and eukaryotic organisms possess large amounts of the microsatellites repeat. Many microsatellites have high mutation rates that generate the high levels of allelic diversity necessary for genetic studies of processes acting on ecological time scales. The high variability of microsatellites provided the foundation for their successful application in a wide range of fundamental and applied fields of biology. However, de novo isolation is needed for most species hence in this study we tried to mine the microsatellite marker using PCR-based isolation of microsatellite arrays (PIMA) on Blue spotted mudskipper, Boleophthalmus boddarti a fish uniquely restricted to coastal and estuarine habitat was also commercially important. Out of three trials, seven microsatellite repeats were detected but only three repeat types (AAG)4, (TCAG)3 and (CT)4 can be useful as microsatellite marker following PHOBOS V3.3.12 analysis. Meanwhile, the detection of octa (AATACAT)2, penta (TGACA)2 and heptanucleotides (GGAGATA)2 were unable to be continued as functional microsatellite marker as there were missense variants and interruptions detected either on forward or reverse strand of the repeat. Thus, PIMA method could be considered as tedious and detected low yields of microsatellite markers. Nevertheless, the conventional method for generating microsatellite markers from PCR based methods could be done with in silico mining of microsatellite sequences from DNA sequence databases or next generation sequencing (NGS).
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Gadgil, Rujuta Yashodhan, Eric J. Romer, Caitlin C. Goodman, S. Dean Rider, French J. Damewood, Joanna R. Barthelemy, Kazuo Shin-ya, Helmut Hanenberg, and Michael Leffak. "Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication." Journal of Biological Chemistry 295, no. 45 (September 1, 2020): 15378–97. http://dx.doi.org/10.1074/jbc.ra120.013495.
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Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG)n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG)n chromosome fragility is repeat length–dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure–prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
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Ishii, T., Y. Xu, and S. R. McCouch. "Nuclear- and chloroplast-microsatellite variation in A-genome species of rice." Genome 44, no. 4 (August 1, 2001): 658–66. http://dx.doi.org/10.1139/g01-044.
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Simple sequence length polymorphism analysis was carried out to reveal microsatellite variation and to clarify the phylogenetic relationships among A-genome species of rice. Total DNA from 29 cultivars (23 Oryza sativa and 6 O. glaberrima) and 30 accessions of wild A-genome species (12 O. rufipogon, 5 O. glumaepatula, 2 O. longistaminata, 6 O. meridionalis, and 5 O. barthii) was used as a template for PCR to detect 24 nuclear and 10 chloroplast microsatellite loci. Microsatellite allelic diversity was examined based on amplified banding patterns. Microsatellites amplified clearly in all 59 accessions, with an average of 18.4 alleles per locus. The polymorphism information content (PIC) value ranged from 0.85 to 0.94, with an average of 0.89. At the species level, high average PIC values were observed in O. sativa (0.79) and O. rufipogon (0.80). For chloroplast microsatellites, the average number of alleles per locus and the average PIC value were 2.9 and 0.38, respectively. While the magnitude of diversity was much greater for nuclear microsatellites than for chloroplast microsatellites, they showed parallel patterns of differentiation for each taxonomic group. Using the ratio of common alleles (estimated as size of amplified fragments) as a similarity index, the average percentages of common microsatellite alleles were calculated between taxa. For both nuclear and chloroplast microsatellites, O. sativa showed the highest similarity values to O. rufipogon, and O. glaberrima was most similar to O. barthii. These data support previous evidence that these cultivars originated from the corresponding wild ancestral species.Key words: simple sequence length polymorphism, SSLP, microsatellite marker, rice, Oryza sativa, allelic diversity, phylogenetics.
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Zhang, Duo, and Haoxiang Wang. "Comparative Analysis of Microsatellite Sequences in Six Gamma-coronaviruses." Highlights in Science, Engineering and Technology 74 (December 29, 2023): 1146–53. http://dx.doi.org/10.54097/rrcvhv94.
Full textAbstract:
Microsatellite sequences are DNA or RNA repeat sequences with 1-6 bases as repeat units, also known as simple repeat sequences, that appear in the genome's non-coding, coding, and intergenic regions. Microsatellite sequences are extremely changeable and varied, and their presence encourages genomic variety and evolution. Gamma-coronavirus is a genus in the Coronaviridae subfamily. Microsatellites are extensively dispersed in gamma-coronavirus genomes' coding and non-coding regions. There are currently few papers on the microsatellite analysis of γ-coronaviruses. The distribution frequency, GC content, and nucleotide repeat sequences of γ-coronavirus SSR were studied in this work using MISA online program and SSRhunter, and three results were drawn: 1.Viruses have a short evolutionary period and a lower variety of microsatellites than prokaryotes and eukaryotes. 2.Type II microsatellites have a significant role in cross-species infection and gene expression differences. 3.Evolution might be skewed. This research will contribute to a better understanding of the structure, function, and evolutionary importance of microsatellites in tiny genomes.
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Johnson, Kirsten M., Nathan R. Mahler, Ranajeet S. Saund, Emily R. Theisen, Cenny Taslim, Nathan W. Callender, Jesse C. Crow, Kyle R. Miller, and Stephen L. Lessnick. "Role for the EWS domain of EWS/FLI in binding GGAA-microsatellites required for Ewing sarcoma anchorage independent growth." Proceedings of the National Academy of Sciences 114, no. 37 (August 28, 2017): 9870–75. http://dx.doi.org/10.1073/pnas.1701872114.
Full textAbstract:
Ewing sarcoma usually expresses the EWS/FLI fusion transcription factor oncoprotein. EWS/FLI regulates myriad genes required for Ewing sarcoma development. EWS/FLI binds GGAA-microsatellite sequences in vivo and in vitro. These sequences provide EWS/FLI-mediated activation to reporter constructs, suggesting that they function as EWS/FLI-response elements. We now demonstrate the critical role of an EWS/FLI-bound GGAA-microsatellite in regulation of the NR0B1 gene as well as for Ewing sarcoma proliferation and anchorage-independent growth. Clinically, genomic GGAA-microsatellites are highly variable and polymorphic. Current data suggest that there is an optimal “sweet-spot” GGAA-microsatellite length (of 18–26 GGAA repeats) that confers maximal EWS/FLI-responsiveness to target genes, but the mechanistic basis for this remains unknown. Our biochemical studies, using recombinant Δ22 (a version of EWS/FLI containing only the FLI portion), demonstrate a stoichiometry of one Δ22-monomer binding to every two consecutive GGAA-repeats on shorter microsatellite sequences. Surprisingly, the affinity for Δ22 binding to GGAA-microsatellites significantly decreased, and ultimately became unmeasureable, when the size of the microsatellite was increased to the sweet-spot length. In contrast, a fully functional EWS/FLI mutant (Mut9, which retains approximately half of the EWS portion of the fusion) showed low affinity for smaller GGAA-microsatellites but instead significantly increased its affinity at sweet-spot microsatellite lengths. Single-gene ChIP and genome-wide ChIP-sequencing (ChIP-seq) and RNA-seq studies extended these findings to the in vivo setting. Together, these data demonstrate the critical requirement of GGAA-microsatellites as EWS/FLI activating response elements in vivo and reveal an unexpected role for the EWS portion of the EWS/FLI fusion in binding to sweet-spot GGAA-microsatellites.
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Moniruzzaman, M., R. Khatun, Zahira Yaakob, M. S. Khan, and A. A. Mintoo. "Development of Microsatellites: A Powerful Genetic Marker." Agriculturists 13, no. 1 (January 24, 2016): 152–72. http://dx.doi.org/10.3329/agric.v13i1.26559.
Full textAbstract:
The tandem repeats, conserved short segments of DNA, which are found in all prokaryotic and eukaryotic genomes, are called microsatellites. It is also known as variable number tandem repeats (VNTRs), simple sequence repeats (SSRs) and short tandem repeats (STRs). Microsatellites present in both coding and non-coding regions of a genome. The high polymorphism of microsatellites makes them powerful genetic markers for genome mapping of many organisms. It is also suitable for ancient and forensic DNA studies for population genetics and conservation of biological resources. The major disadvantage of microsatellites is that for the first time they need to be isolated de novo from most species being examined. The task of microsatellite isolation is quite cumbersome involving in terms of effort and time, because it traditionally involves screening of genomic libraries. Cross-species amplification, Mining microsatellites from nucleotide sequenced data and Genomic library- based method are general methods of microsatellite isolation. Cross-species method may not effective for all species, Data mining is not applicable if there is no or limited data of DNA sequence. Genomic library based method is the best choice. Traditional protocol, primer extension protocol, selective hybridization, and Fast Isolation by AFLP of Sequences containing repeats (FIASCO) are the protocols of microsatellite development based on genomic library. FIASCO is the best protocol ever developed.The Agriculturists 2015; 13(1) 152-172
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Wang, Ying, Mingjie Chen, Hong Wang, Jing-Fang Wang, and Dapeng Bao. "Microsatellites in the Genome of the Edible Mushroom,Volvariella volvacea." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/281912.
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Using bioinformatics software and database, we have characterized the microsatellite pattern in theV. volvaceagenome and compared it with microsatellite patterns found in the genomes of four other edible fungi:Coprinopsis cinerea,Schizophyllum commune,Agaricus bisporus,andPleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in theV. volvaceagene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides) outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes.
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Bae, Jin H., and David Yu Zhang. "Predicting stability of DNA bulge at mononucleotide microsatellite." Nucleic Acids Research 49, no. 14 (July 26, 2021): 7901–8. http://dx.doi.org/10.1093/nar/gkab616.
Full textAbstract:
Abstract Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. Stability of such dynamic bulges, however, is still poorly understood despite their critical role in cancer genomics and neurological disease studies. In this paper, we have built a model that predicts the thermodynamics of a sliding bulge at a microsatellite. We first identified 40 common bulge states that can be assembled into any sliding bulges, and then characterized them with toehold exchange energy measurement and the partition function. Our model, which is the first to predict the free energy of sliding bulges with more than three repeats, can infer the stability penalty of a sliding bulge of any sequence and length with a median prediction error of 0.22 kcal/mol. Patterns from the prediction clearly explain landscapes of microsatellites observed in the literature, such as higher mutation rates of longer microsatellites and C/G microsatellites.
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Sharma, P. C., Manish Roorkiwal, and Atul Grover. "Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome." International Journal of Evolutionary Biology 2012 (September 13, 2012): 1–8. http://dx.doi.org/10.1155/2012/970920.
Full textAbstract:
Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1 Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome.
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PANDEY, Saumy, Vinay SHARMA, and Afroz ALAM. "Potential of Microsatellites Markers for the Genetic Analysis of Bryophytes." Notulae Scientia Biologicae 8, no. 1 (March 16, 2016): 37–46. http://dx.doi.org/10.15835/nsb819748.
Full textAbstract:
Microsatellites have increasingly being used to study genetic diversity, phylogeny, population genetics, population ecology and genetic mapping of bryophytes. Due to co-dominant and highly reproducible features, microsatellites became markers of choice for several genetic analyses of bryophytes. However, the major limitation is de novo isolation of microsatellites from the interest species which were studied and gave genomic libraries. Initially, traditional methods of microsatellite development were tedious and time consuming, but due to the sequencing of several bryophytes available in public databases, advancement in PCR technologies and computer software, have cumulatively facilitated the development of microsatellites for bryophytes study. This review examines the features, strategies for the development of microsatellites and their utilization in many aspects of genetic and ecological studies of bryophytes.
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McConnell, Stewart K., Patrick O'Reilly, Lorraine Hamilton, Jonathan M. Wright, and Paul Bentzen. "Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations." Canadian Journal of Fisheries and Aquatic Sciences 52, no. 9 (September 1, 1995): 1863–72. http://dx.doi.org/10.1139/f95-779.
Full textAbstract:
Atlantic salmon populations show low levels of genetic differentiation relative to other salmonid species, when surveyed by allozymes, and with mitochondrial DNA and nuclear ribosomal DNA markers. Here we report the application of three novel microsatellite VNTR loci to population differentiation in Atlantic salmon. A total of 232 microsatellites, cloned from Atlantic salmon, were classified as perfect, imperfect, and compound repeats. Microsatellite length, as in other teleosts, was significantly larger than published mammalian microsatellites. Primers for PCR amplification of three salmon microsatellites were designed. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for five populations from Nova Scotia, Canada, and from Europe. Nei's genetic distances of 0.02–0.9 were observed among populations. There was a clear discrimination between Canadian and European fish based on unique alleles present at two loci. These Atlantic salmon primers also amplify presumably homologous loci in nine other salmonid species. The polymorphic microsatellites loci reported here demonstrate great potential as genetic markers in population, breeding, and evolutionary studies.
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Beacham, Terry D., B. McIntosh, and C. Wallace. "A comparison of stock and individual identification for sockeye salmon (Oncorhynchus nerka) in British Columbia provided by microsatellites and single nucleotide polymorphisms." Canadian Journal of Fisheries and Aquatic Sciences 67, no. 8 (August 2010): 1274–90. http://dx.doi.org/10.1139/f10-061.
Full textAbstract:
Variation at 14 microsatellite loci, one major histocompatibility complex (MHC) locus, and 49 single nucleotide polymorphism (SNPs) loci was surveyed in 44 populations of sockeye salmon ( Oncorhynchus nerka ) over 16 regions from southern and central British Columbia, Canada. Sequential addition of the five highest rated SNPs to the suite of 14 microsatellites provided the equivalent average accuracy when compared with the current suite of microsatellites and MHC. Six microsatellites provided the equivalent average stock identification resolution and individual assignment accuracy compared with 46 SNPs. For regional stock compositions, 53–104 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. For population-specific stock compositions, 75–79 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. Equivalency in individual assignment accuracy to region was estimated to require 100 SNPs of the quality evaluated in the study, whereas equivalent accuracy in assignment to specific populations was estimated to require 124 SNPs. Applications that incorporate the existing power of a combined microsatellite–SNP approach are the best current technique available for sockeye salmon stock identification applications in southern British Columbia.
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Avvaru, Akshay Kumar, Deepak Sharma, Archana Verma, Rakesh K. Mishra, and Divya Tej Sowpati. "MSDB: a comprehensive, annotated database of microsatellites." Nucleic Acids Research 48, no. D1 (October 10, 2019): D155—D159. http://dx.doi.org/10.1093/nar/gkz886.
Full textAbstract:
Abstract Microsatellites are short tandem repeats of 1–6 nucleotide motifs, studied for their utility as genome markers and in forensics. Recent evidence points to the role of microsatellites in important regulatory functions, and their length polymorphisms at coding regions are linked to various neurodegenerative disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and their evolution remains poorly understood. Though other databases of microsatellites exist, they fall short on several fronts. MSDB (MicroSatellite DataBase) is a collection of >4 billion microsatellites from 37 680 genomes presented in a user-friendly web portal for easy, interactive analysis and visualization. This is by far the most comprehensive, annotated, updated database to access and analyze microsatellite data of multiple species. The features of MSDB enable users to explore the data as tables that can be filtered and exported, and also as interactive charts to view and compare the data of multiple species simultaneously. Its modularity and architecture permit seamless updates with new data, making it a powerful tool and useful resource to researchers working on this important class of DNA elements, particularly in context of their evolution and emerging roles in genome organization and gene regulation.
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Pfeiffer, Antonella, Angelo M. Olivieri, and Michele Morgante. "Identification and characterization of microsatellites in Norway spruce (Picea abies K.)." Genome 40, no. 4 (August 1, 1997): 411–19. http://dx.doi.org/10.1139/g97-055.
Full textAbstract:
Norway spruce (Picea abies) genomic libraries were screened for presence of dinucleotide AC/GT and AG/CT microsatellites (or simple sequence repeats). On average, one (AG)n microsatellite every 194 kb and one (AC)n microsatellite every 406 kb were found. Forty-six positive clones were sequenced and primers flanking 24 AG microsatellites and 12 AC microsatellites designed. Only seven (20%) of them produced the expected single-locus polymorphic pattern when used to amplify Norway spruce DNAs. The other primer pairs gave either multiple bands or bad amplification, or a single monomorphic fragment. Such a small proportion of successful primer pairs was attributed to the high level of complexity of the Norway spruce genome. Dot blot analysis of the clones showed that many of them contained repetitive DNA and that those giving the single-locus polymorphic patterns usually corresponded to single-copy sequences. A family of repetitive DNA that contained AG repeats was identified and was present in about 40 000 copies per haploid genome. Simple Mendelian inheritance was observed for all the polymorphisms tested. The average number of alleles was 13, ranging from 6 to 22, and the expected heterozygosity was 0.79 when seven microsatellites were used to genotype a panel of 18 trees representing different populations. Compared with isozymes, microsatellites are about five times more informative and could provide an extremely valuable source of markers for genome mapping and genetic diversity studies.Key words: microsatellite, repetitive DNA, hypervariability, Picea abies, genome complexity.
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Korom, E., K. Bakos, G. Veress, O. Pinke, K. M. Reed, L. Varga, and B. Kovács. "Isolation of 11 new polymorphic microsatellites from CA enriched turkey genomic libraries (Short communication)." Archives Animal Breeding 53, no. 5 (October 10, 2010): 618–22. http://dx.doi.org/10.5194/aab-53-618-2010.
Full textAbstract:
Abstract. Microsatellite loci from the ancient Hungarian variety of the Broad Breasted Bronze Turkey (Meleagris gallopavo) were isolated. CA-repeat enriched libraries were constructed from DNA of randomly collected samples. Libraries were screened for repeat-containing clones by PIMA (PCR Isolation of Microsatellite Arrays) and the DNA-sequence of 167 positive clones was determined. A total of 136 microsatellite repeat-containing sequences were found, 59 sequences were unique. Comparing these with the genomic databases, we found 7 previously annotated microsatellite sequences. The newly isolated 52 microsatellites were tested on the mapping population of the University of Minnesota, and the map position of 11 microsatellites was determined.
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Rogge, Ryan, Taylor Patterson, Alicia Navetta, and Dhruti Legare. "Abstract 2943: Investigation of microsatellite instability in RNA compared to DNA, using microsatellite targeted, anchored multiplex PCR and NGS." Cancer Research 84, no. 6_Supplement (March 22, 2024): 2943. http://dx.doi.org/10.1158/1538-7445.am2024-2943.
Full textAbstract:
Abstract MSI measurements are typically made on DNA, but it would be useful to make similar measurements from RNA or total nucleic acid inputs (TNA), so that MSI determinations could be made in parallel to interrogation of the RNA. Doing so requires characterizations of microsatellite lengths from those which are transcribed and untranscribed, because both will be detected following cDNA creation. Microsatellite instability (MSI) occurs when small unit repeats of DNA undergo incorrect replication resulting in the growth or contraction of the number of repeats in the newly synthesized DNA. This accumulation of errors at microsatellite DNA is usually mitigated by the mismatch repair (MMR) pathway which can correct these errors. MSI is of interest because it serves as a phenotypic readout of the status of the MMR machinery, and MSI status can correlate to tumor progression and response to agents that regulate these cellular mechanisms. We investigated the status of microsatellites using Anchored Multiplex PCR (AMP™) targeted panels (RUO) and compared results from TNA inputs using an AMP MSI module and both VARIANTPlex™ chemistry to interrogate DNA, and FUSIONPlex™ chemistry to interrogate both RNA + DNA. Our results indicate differences in the diversity of lengths of microsatellites present in RNA, and the resulting stability calls which would be made at those sites. Microsatellite length diversity was highly dependent on the genomic context of the microsatellite. Microsatellites located within transcripts showed increased length diversity when examining the RNA + DNA results compared to DNA alone. Microsatellites located in intergenic regions, which are unlikely to be transcribed, showed no increase in diversity of lengths when comparing the RNA + DNA results to DNA alone. While these results suggest that MSI determinations could be made from RNA or RNA + DNA NGS data, the unique behavior of microsatellites in RNA is likely to require additional investigations and unique data analysis techniques to correctly categorize microsatellites as stable or unstable. Confidential - Company Proprietary Citation Format: Ryan Rogge, Taylor Patterson, Alicia Navetta, Dhruti Legare. Investigation of microsatellite instability in RNA compared to DNA, using microsatellite targeted, anchored multiplex PCR and NGS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2943.
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Campomayor, Nicole Bon, Nomar Espinosa Waminal, Byung Yong Kang, Thi Hong Nguyen, Soo-Seong Lee, Jin Hoe Huh, and Hyun Hee Kim. "Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites." Cells 10, no. 9 (September 8, 2021): 2358. http://dx.doi.org/10.3390/cells10092358.
Full textAbstract:
Intergeneric crosses between Brassica species and Raphanus sativus have produced crops with prominent shoot and root systems of Brassica and R. sativus, respectively. It is necessary to discriminate donor genomes when studying cytogenetic stability in distant crosses to identify homologous chromosome pairing, and microsatellite repeats have been used to discriminate subgenomes in allopolyploids. To identify genome-specific microsatellites, we explored the microsatellite content in three Brassica species (B. rapa, AA, B. oleracea, CC, and B. nigra, BB) and R. sativus (RR) genomes, and validated their genome specificity by fluorescence in situ hybridization. We identified three microsatellites showing A, C, and B/R genome specificity. ACBR_msat14 and ACBR_msat20 were detected in the A and C chromosomes, respectively, and ACBR_msat01 was detected in B and R genomes. However, we did not find a microsatellite that discriminated the B and R genomes. The localization of ACBR_msat20 in the 45S rDNA array in ×Brassicoraphanus 977 corroborated the association of the 45S rDNA array with genome rearrangement. Along with the rDNA and telomeric repeat probes, these microsatellites enabled the easy identification of homologous chromosomes. These data demonstrate the utility of microsatellites as probes in identifying subgenomes within closely related Brassica and Raphanus species for the analysis of genetic stability of new synthetic polyploids of these genomes.
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Wenne, Roman. "Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations." Genes 14, no. 4 (March 27, 2023): 808. http://dx.doi.org/10.3390/genes14040808.
Full textAbstract:
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
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Gao, Caihua, Xiaodong Ren, Annaliese S. Mason, Jiana Li, Wei Wang, Meili Xiao, and Donghui Fu. "Revisiting an important component of plant genomes: microsatellites." Functional Plant Biology 40, no. 7 (2013): 645. http://dx.doi.org/10.1071/fp12325.
Full textAbstract:
Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.
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Scotti, I., F. Magni, R. Fink, W. Powell, G. Binelli, and P. E. Hedley. "Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences." Genome 43, no. 1 (February 1, 2000): 41–46. http://dx.doi.org/10.1139/g99-095.
Full textAbstract:
A Norway spruce (Picea abies K.) cDNA library obtained from vegetative bud tissue was screened for the presence of (AG)n and (AC)n microsatellite repeats. Ten (AG)n and six (AC)n microsatellites were found, with an average length of 25.5 repeat units. Most of the microsatellites are simple perfect repeats. The microsatellite distribution within the clones is clearly non-random, with different classes of repeats lying in different positions relative to the coding region and in a highly conserved orientation. An estimate of the frequency of dinucleotide microsatellites in expressed regions was obtained, showing that SSRs (simple sequence repeats) are found in genes about 20 times less frequently than in random genomic clones, with (AG)n repeats more frequent than (AC)n repeats. Potential applications of these sequences as expressed region-based molecular markers are shown by developing six SSR markers for the detection of natural variation in Norway spruce populations and testing two of them for the identification of illegitimate progenies from a mapping population. Key words: Picea abies, microsatellites, SSRs, ESTs, population genetics, trees.
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Hadonou, A. M., D. J. Sargent, F. Wilson, C. M. James, and D. W. Simpson. "Development of microsatellite markers in Fragaria, their use in genetic diversity analysis, and their potential for genetic linkage mapping." Genome 47, no. 3 (June 1, 2004): 429–38. http://dx.doi.org/10.1139/g03-142.
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We have developed 21 new microsatellites in the model diploid perennial species Fragaria vesca from an enriched genomic library developed using F. vesca 'Ruegen'. The transferability of the primer pairs to other Fragaria species was high; all 31 primer pairs produced amplicons in 3 accessions of the octoploid strawberry Fragaria × ananassa, whereas 24 (77%) amplified a product in 7 other diploid Fragaria species. We analysed the allelic variation among 15 F. vesca accessions using the 21 microsatellites reported here and 10 F. vesca microsatellites described previously. The level of polymorphism detected at these microsatellite loci was high; five loci were monomorphic. Only two microsatellites were required to unambiguously discriminate among the 15 F. vesca accessions. A preliminary survey of segregation in an F2 progeny indicates that 20 of the 26 polymorphic loci (77%) could be mapped.Key words: Fragaria, genetic fingerprinting, microsatellites.
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Mathema, Vivek Bhakta, Supatchara Nakeesathit, Nicholas J. White, Arjen M. Dondorp, and Mallika Imwong. "Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi." Parasite 27 (2020): 34. http://dx.doi.org/10.1051/parasite/2020034.
Full textAbstract:
Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1–10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18–29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms “cell parts,” “binding,” “developmental processes,” and “metabolic processes.” The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology.
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Ming, Yao, Xueying Yu, Wei Liu, Jingzhen Wang, and Wenhua Liu. "The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation." Journal of Marine Science and Engineering 10, no. 6 (June 20, 2022): 834. http://dx.doi.org/10.3390/jmse10060834.
Full textAbstract:
Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.
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Piscor, Diovani, and Patricia P. Parise-Maltempi. "Microsatellite Organization in the B Chromosome and A Chromosome Complement in Astyanax (Characiformes, Characidae) Species." Cytogenetic and Genome Research 148, no. 1 (2016): 44–51. http://dx.doi.org/10.1159/000444728.
Full textAbstract:
The organization of microsatellites in B and sex chromosomes has been linked to chromosomal evolution in a number of animal groups. Here, the chromosomal organizations of (CA)15, (GA)15, (CG)15, (GACA)4, and (GATA)8 microsatellites were examined in several Astyanax species with different diploid numbers: Astyanax mexicanus (2n = 50 + 1 B chromosome), A. altiparanae (2n = 50), A. marionae (2n = 48), A. fasciatus (2n = 46), and A. schubarti (2n = 36). The (CA)15 and (GA)15 microsatellites were dispersed across the chromosomes of A. altiparanae and A. fasciatus but were also observed as clusters (CA and GA for A. altiparanae, and CA for A. fasciatus). In A. marionae and A. schubarti, the (CA)15 and (GA)15 microsatellites were dispersed but were also observed as clustered signals and coincident with heterochromatic regions. In all 4 of these species, the (CG)15 and (GACA)4 microsatellites were dispersed across chromosomes, and the (GATA)8 microsatellite was co-localized with 5S rDNA. In A. mexicanus, the (CA)15, (GA)15, (CG)15, (GATA)8, and (GACA)4 microsatellites were weakly detected and dispersed across the chromosomes of the A complement. On the B chromosome, signals for the different microsatellites were weak, strong, absent, weak, and absent, respectively. The distribution of microsatellites and the locational relationship between microsatellites and 5S rDNA are discussed, and a possible evolutionary pathway is proposed for microsatellites in Astyanax.
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Haiduk, Tiffany, Michael Brockmann, Christoph Schmitt, Ramona-Liza Tillmann, Monika Pieper, Jessica Lüsebrink, Oliver Schildgen, and Verena Schildgen. "Are Microsatellite Patterns Specific for Tumor Types? A Pilot Investigation." Journal of Molecular Pathology 1, no. 1 (September 4, 2020): 3–8. http://dx.doi.org/10.3390/jmp1010002.
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Microsatellite testing is an emerging field of molecular pathology, as microsatellite instability (MSI) appears to be a predictive biomarker for some cancers. Although multiple studies on microsatellites have been published, recent observations suggest that the microsatellites that define instability differ between tumor entities. This assumption is confirmed by the present study that compared different MSI assays validated for colorectal cancer. Whilst all assays deliver the same MSI/MSS status for colorectal cancers, they differ for tonsillar tumors, leading to the hypothesis that MSI patterns are tumor-type specific.
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Russell, Joanne, John Fuller, George Young, Bill Thomas, Malcolm Macaulay, Robbie Waugh, Wayne Powell, and Graziana Taramino. "Discriminating between barley genotypes using microsatellite markers." Genome 40, no. 4 (August 1, 1997): 442–50. http://dx.doi.org/10.1139/g97-059.
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Eleven microsatellite loci were used to survey 24 barley genotypes representing 23 cultivars and a breeding line in official trials. Three separate combinations of four microsatellites had overall probabilities of identity of less than 1 in 1000 and could distinguish between all 24 barley genotypes. It is shown that the microsatellites could distinguish genotypes with the same pedigree and also that patterns of discrimination were different from those obtained from botanical descriptors. The stability of microsatellites across different generations was demonstrated by a retrospective analysis of the pedigree of Golden Promise. One of the parents of Maythorpe, the immediate ancestor of Golden Promise, was shown to be Irish Goldthorpe rather than Goldthorpe, thereby resolving conflicting published pedigrees.Key words: barley, microsatellites, cultivar identification, stability, Golden Promise.
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Reddy, K. Damodar, E. G. Abraham, and J. Nagaraju. "Microsatellites in the silkworm, Bombyx mori: Abundance, polymorphism, and strain characterization." Genome 42, no. 6 (December 1, 1999): 1057–65. http://dx.doi.org/10.1139/g99-027.
Full textAbstract:
We have isolated and characterized microsatellites (simple sequence repeat (SSR) loci) from the silkworm genome. The screening of a partial genomic library by the conventional hybridization method led to the isolation of 28 microsatellites harbouring clones. The abundance of (CA)n repeats in the silkworm genome was akin to those reported in the other organisms such as honey bee, pig, and human, but the (CT)n repeat motif is less common compared to bumble bee and honey bee genomes. Detailed analysis of 13 diverse silkworm strains with a representative of 15 microsatellite loci revealed a number of alleles ranging from 3 to 17 with heterozygosity values of 0.66-0.90. Along with strain-specific microsatellite markers, diapause and non-diapause strain-specific alleles were also identified. The repeat length did not show any relationship with the degree of polymorphism in the present study. The co-dominant inheritance of microsatellite markers was demonstrated in F1 offspring. A list of primer sequences that tag each locus is provided. The availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in silkworm.Key words: microsatellites, simple sequence repeats, polymorphisms, silkworm strains, Bombyx mori.
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Wu, Shuangcheng, Hang Ye, Yuansong Chen, Jiemei Deng, Jiexia Su, Yayu Xie, Qinru Xie, et al. "Characterization and cross-species transferability of a novel set of microsatellites derived from root transcriptomes of Camellia oleifera." Plant Genetic Resources: Characterization and Utilization 17, no. 04 (February 21, 2019): 371–74. http://dx.doi.org/10.1017/s1479262119000066.
Full textAbstract:
AbstractCamellia oleifera is an important woody plant producing healthy edible oils. People need a large number of molecular markers, especially microsatellite, in breeding of C. oleifera. In this study, we sequenced the root transcriptomes of C. oleifera, and then designed a novel set of microsatellite markers based on the root-expressed genes. We assembled a total of 57,121 unigenes with a length of 42.63 Mb, which harboured 15,902 microsatellites. Among these microsatellites, di-nucleotide repeat motifs were the most abundant group (56.45%), then followed by tri- (25.20%), mono- (12.12%), hexa- (3.21%), penta- (2.18%) and quad-nucleotide ones (0.84%). In total, 6738 primer pairs were designed successfully to amplify the microsatellite loci. To test these microsatellite markers, 48 primer pairs were randomly selected and synthesized and validated in C. oleifera and its eight relatives. Up to 75% of the primer pairs amplified in C. oleifera and its relatives, and 62.5% displayed polymorphism. The transferability and diverse alleles across its eight relatives were detected for each polymorphic primer pair. The novel set of microsatellites derived from the root transcriptomes here provided a useful resource for future molecular genetics improvement of C. oleifera and its relatives.
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Ranathunge, Chathurani, Sreepriya Pramod, Sébastien Renaut, Gregory L. Wheeler, Andy D. Perkins, Loren H. Rieseberg, and Mark E. Welch. "Microsatellites as Agents of Adaptive Change: An RNA-Seq-Based Comparative Study of Transcriptomes from Five Helianthus Species." Symmetry 13, no. 6 (May 24, 2021): 933. http://dx.doi.org/10.3390/sym13060933.
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Mutations that provide environment-dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally significant variation. Some proposed mechanisms that explore the role of cis-regulatory mutations in gene expression divergence involve microsatellites. Microsatellites exhibit high mutation rates achieved through symmetric or asymmetric mutation processes and are abundant in both coding and non-coding regions in positions that could influence gene function and products. Here we tested the hypothesis that microsatellites contribute to gene expression divergence among species with 50 individuals from five closely related Helianthus species using an RNA-seq approach. Differential expression analyses of the transcriptomes revealed that genes containing microsatellites in non-coding regions (UTRs and introns) are more likely to be differentially expressed among species when compared to genes with microsatellites in the coding regions and transcripts lacking microsatellites. We detected a greater proportion of shared microsatellites in 5′UTRs and coding regions compared to 3′UTRs and non-coding transcripts among Helianthus spp. Furthermore, allele frequency differences measured by pairwise FST at single nucleotide polymorphisms (SNPs), indicate greater genetic divergence in transcripts containing microsatellites compared to those lacking microsatellites. A gene ontology (GO) analysis revealed that microsatellite-containing differentially expressed genes are significantly enriched for GO terms associated with regulation of transcription and transcription factor activity. Collectively, our study provides compelling evidence to support the role of microsatellites in gene expression divergence.
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Ho, Eddie K. H., Fenner Macrae, Leigh C. Latta, Maia J. Benner, Cheng Sun, Dieter Ebert, and Sarah Schaack. "Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna." Molecular Biology and Evolution 36, no. 9 (May 11, 2019): 1942–54. http://dx.doi.org/10.1093/molbev/msz118.
Full textAbstract:
Abstract Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species, and have rarely been compared across genotypes and populations within a species. Here, we investigate the dynamics of microsatellite mutation over long- and short-time periods by quantifying the starting abundance and mutation rates for microsatellites for six different genotypes of Daphnia magna, an aquatic microcrustacean, collected from three populations (Finland, Germany, and Israel). Using whole-genome sequences of these six starting genotypes, descendent mutation accumulation (MA) lines, and large population controls (non-MA lines), we find each genotype exhibits a distinctive initial microsatellite profile which clusters according to the population-of-origin. During the period of MA, we observe motif-specific, highly variable, and rapid microsatellite mutation rates across genotypes of D. magna, the average of which is order of magnitude greater than the recently reported rate observed in a single genotype of the congener, Daphnia pulex. In our experiment, genotypes with more microsatellites starting out exhibit greater losses and those with fewer microsatellites starting out exhibit greater gains—a context-dependent mutation bias that has not been reported previously. We discuss how genotype-specific mutation rates and spectra, in conjunction with evolutionary forces, can shape both the differential accumulation of repeat content in the genome and the evolution of mutation rates.
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Abdul-Muneer, P. M. "Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies." Genetics Research International 2014 (April 7, 2014): 1–11. http://dx.doi.org/10.1155/2014/691759.
Full textAbstract:
Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management.
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Wada, C., S. Shionoya, Y. Fujino, H. Tokuhiro, T. Akahoshi, T. Uchida, and H. Ohtani. "Genomic instability of microsatellite repeats and its association with the evolution of chronic myelogenous leukemia [see comments]." Blood 83, no. 12 (June 15, 1994): 3449–56. http://dx.doi.org/10.1182/blood.v83.12.3449.3449.
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Abstract Tumorigenesis has been shown to proceed through a series of genetic alterations involving protooncogenes and tumor-suppressor genes. Investigation of genomic instability of microsatellites has indicated a new mechanism for human carcinogenesis in hereditary nonpolyposis colorectal cancer and sporadic cancer and this instability has been shown to be related to inherited predisposition to cancer. This study was conducted to determine whether such microsatellite instability is associated with the evolution of chronic myelogenous leukemia (CML) to the blast crisis. Nineteen CML patients clinically progressing from the chronic phase to accelerated phase or blast crisis and 20 other patients in the CML chronic phase were studied. By polymerase chain reaction assay, DNAs for genomic instability in five separate microsatellites in chromosome arms 5q (Mfd27), 17p (Mfd41), 18q (DCC), 3p (CI3–9), and 8p (LPL) were examined. Differences in unrelated microsatellites of chronic and blastic phase DNAs in 14 of 19 patients (73.7%) were demonstrated. Somatic instability in five microsatellites, Mfd27, Mfd41, DCC, CI3–9, and LPL, was detected in 2 of 19 (10.5%), 8 of 19 (42.1%), 11 of 19 (57.9%), 4 of 17 (23.5%), and 4 of 17 (23.5%) cases. In 10 of 19 cases (52.6%), genetic instability in at least two of five microsatellites was observed and was categorized as replication error (RER+) phenotype. CML evolution cases with myeloid, lymphoid, and mixed phenotypes and the blast crisis and accelerated phase showed somatic instability in a number of microsatellites. No alterations in leukemic cells at the chronic phase could be detected in any microsatellites. These data indicate instability of microsatellites (RER+) but not familial predisposition to possibly be a late genetic event in the evolution of CML to blast crisis. In the microsatellite of the DCC gene, complicated alterations in band patterns caused by instability as well as loss of heterozygosity (LOH) were observed in 13 of 19 cases (68.4%): instability in 9 cases, instability plus LOH in 2 cases, and only LOH in 2 cases. These highly frequent alterations in microsatellites, including instability and LOH, suggesting that secondary events due possibly to loss of fidelity in replication and repair machinery may be significantly associated with CML evolution.