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Artykuły w czasopismach na temat „Microsatellites”

Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 25 lipca 2025

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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 (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 majori

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2

Harker, N., L. R. Rampling, M. R. Shariflou, et al. "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

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3

Yu, Kangfu, Soon J. Park, and Vaino Poysa. "Abundance and variation of microsatellite DNA sequences in beans (Phaseolus andVigna)." Genome 42, no. 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

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4

England, Phillip R., David A. Briscoe, and Richard Frankham. "Microsatellite polymorphisms in a wild population of Drosophila melanogaster." Genetical Research 67, no. 3 (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 g

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5

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

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6

Areshchenkova, Tatyana, and Martin W. Ganal. "Long tomato microsatellites are predominantly associated with centromeric regions." Genome 42, no. 3 (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 m

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7

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

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8

Kaur, Simerpreet. "Microsatellite diversity in four cultivated species of Actinidiaceae and Rutaceae." Bioinformation 19, no. 3 (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, r

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Gobily, Eman, Shimaa Kandel, Hadeer Auoda, Radwa Ahmed, and Mostafa Helal. "Whole-Genome Characterization and Analysis of Microsatellites in Turkey (Meleagris gallopavo) through in silico Approach." Biotecnia 27 (February 28, 2025): e2455. https://doi.org/10.18633/biotecnia.v27.2455.

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Turkey (Meleagris gallopavo) is the second largest contributor in poultry meat production after chickens. The study of microsatellite organization and distribution is of highly important in genomics and evolutionary students. The in silico mining for microsatellites leverages the power of computational biology to streamline and enhance the discovery of microsatellite markers, and reduce the cost of microsatellite detection. This study aimed at in silico mining microsatellite loci in the genome of domestic turkey. Reference sequences of the different chromosome obtained from NBCI and analyzed u

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10

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 intersperse

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11

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 (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,

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12

Kaundun, Shiv Shankhar, and Satoru Matsumoto. "Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis." Genome 45, no. 6 (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

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13

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 (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 (&gt;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 persisten

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14

Anand, Khushbu, Sonu Kumar, Afroz Alam, and Asheesh Shankar. "Mining of microsatellites in mitochondrial genomes of order Hypnales (Bryopsida)." Plant Science Today 6, sp1 (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

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15

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 (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

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Masuzaki, Shinichi, Naoyuki Araki, Naoki Yamauchi, et al. "Chromosomal Locations of Microsatellites in Onion." HortScience 41, no. 2 (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 an

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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 (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

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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 (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 bet

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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 (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

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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 (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 he

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Gadgil, Rujuta Yashodhan, Eric J. Romer, Caitlin C. Goodman, et al. "Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication." Journal of Biological Chemistry 295, no. 45 (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

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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 (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 acc

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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.

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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

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Johnson, Kirsten M., Nathan R. Mahler, Ranajeet S. Saund, et al. "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 (2017): 9870–75. http://dx.doi.org/10.1073/pnas.1701872114.

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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 vari

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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 (2016): 152–72. http://dx.doi.org/10.3329/agric.v13i1.26559.

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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

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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 regi

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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 (2016): 37–46. http://dx.doi.org/10.15835/nsb819748.

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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 publi

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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 (2021): 7901–8. http://dx.doi.org/10.1093/nar/gkab616.

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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

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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.

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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 duplicate

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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 (1995): 1863–72. http://dx.doi.org/10.1139/f95-779.

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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 mi

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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 (2010): 1274–90. http://dx.doi.org/10.1139/f10-061.

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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 wit

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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 (2019): D155—D159. http://dx.doi.org/10.1093/nar/gkz886.

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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 &gt;4

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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 (1997): 411–19. http://dx.doi.org/10.1139/g97-055.

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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

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Korom, E., K. Bakos, G. Veress, et al. "Isolation of 11 new polymorphic microsatellites from CA enriched turkey genomic libraries (Short communication)." Archives Animal Breeding 53, no. 5 (2010): 618–22. http://dx.doi.org/10.5194/aab-53-618-2010.

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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 isolat

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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 (2024): 2943. http://dx.doi.org/10.1158/1538-7445.am2024-2943.

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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

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Gao, Caihua, Xiaodong Ren, Annaliese S. Mason, et al. "Revisiting an important component of plant genomes: microsatellites." Functional Plant Biology 40, no. 7 (2013): 645. http://dx.doi.org/10.1071/fp12325.

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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

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Wenne, Roman. "Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations." Genes 14, no. 4 (2023): 808. http://dx.doi.org/10.3390/genes14040808.

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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 ha

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Campomayor, Nicole Bon, Nomar Espinosa Waminal, Byung Yong Kang, et al. "Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites." Cells 10, no. 9 (2021): 2358. http://dx.doi.org/10.3390/cells10092358.

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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

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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 (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 polymorphi

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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 (2000): 41–46. http://dx.doi.org/10.1139/g99-095.

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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 o

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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.

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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.

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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 (2022): 834. http://dx.doi.org/10.3390/jmse10060834.

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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 con

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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.

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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

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Russell, Joanne, John Fuller, George Young, et al. "Discriminating between barley genotypes using microsatellite markers." Genome 40, no. 4 (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

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Haiduk, Tiffany, Michael Brockmann, Christoph Schmitt, et al. "Are Microsatellite Patterns Specific for Tumor Types? A Pilot Investigation." Journal of Molecular Pathology 1, no. 1 (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 patter

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Safaa, Hosam M., Mostafa Helal, Seif Yasser, et al. "Genome-Wide In Silico Analysis of Microsatellite Loci in Rabbits." Animals 14, no. 24 (2024): 3659. https://doi.org/10.3390/ani14243659.

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This study aimed to characterize microsatellites in the rabbit genome using an in silico approach and to develop and validate microsatellite markers. Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). The GMATA software was used to define SSRs in the extracted sequences. Twelve primer pairs were used to validate the loci identified and the primers developed. The total number of the detected microsatellite loci overall chromosomes was 1,136,253. The di-nucleotide microsatellite repeats dominated and exceeded 88% of the detected microsatellites in all chr

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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 (1999): 1057–65. http://dx.doi.org/10.1139/g99-027.

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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

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Wu, Shuangcheng, Hang Ye, Yuansong Chen, 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 (2019): 371–74. http://dx.doi.org/10.1017/s1479262119000066.

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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%), h

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Ranathunge, Chathurani, Sreepriya Pramod, Sébastien Renaut, et al. "Microsatellites as Agents of Adaptive Change: An RNA-Seq-Based Comparative Study of Transcriptomes from Five Helianthus Species." Symmetry 13, no. 6 (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 proc

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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.

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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

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