scholarly journals BanSatDB, a whole-genome-based database of putative and experimentally validated microsatellite markers of three Musa species

2018 ◽  
Vol 6 (6) ◽  
pp. 642-650
Author(s):  
Vasu Arora ◽  
Neera Kapoor ◽  
Samar Fatma ◽  
Sarika Jaiswal ◽  
Mir Asif Iquebal ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Whole Genome ◽  
Musa Species

Development and genetic mapping of microsatellite markers from whole genome shotgun sequences in Brassica oleracea

2010 ◽  
Vol 28 (4) ◽  
pp. 585-596 ◽  
Author(s):  
Haitao Li ◽  
Xun Chen ◽  
Yuan Yang ◽  
Jinsong Xu ◽  
Jianxun Gu ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Microsatellite Markers ◽  
Brassica Oleracea ◽  
Whole Genome Shotgun ◽  
Whole Genome

scholarly journals Microsatellite Scan Identifies New Candidate Genes for Susceptibility to Alcoholic Chronic Pancreatitis in Japanese Patients

2008 ◽  
Vol 25 (3) ◽  
pp. 175-180 ◽  
Author(s):  
Kei Kitahara ◽  
Shigeyuki Kawa ◽  
Yoshihiko Katsuyama ◽  
Takeji Umemura ◽  
Yayoi Ozaki ◽  
...  
Keyword(s):  
Chronic Pancreatitis ◽  
Microsatellite Markers ◽  
Candidate Genes ◽  
Disease Susceptibility ◽  
Japanese Patients ◽  
Whole Genome ◽  
Common Risk Factor ◽  
Average Spacing ◽  
Alcoholic Chronic Pancreatitis ◽  
Polymorphic Microsatellite

Alcohol abuse is one of the most common risk factor for chronic pancreatitis, but the underlying pathophysiological mechanisms remain unclear. The aim of this study was to identify genes that contribute to susceptibility or resistance for alcoholic chronic pancreatitis by screening the whole genome. Sixty-five patients with alcoholic chronic pancreatitis (63 men and 2 women, mean age 55.2 years) and 99 healthy Japanese controls were enrolled in this study. This was an association study using 400 polymorphic microsatellite markers with an average spacing of 10.8 cM distributed throughout the whole genome. This search revealed 10 candidate susceptibility regions and 5 candidate resistant regions throughout the genome. No specific microsatellite markers were detected in association with previously reported susceptibility genes for chronic pancreatitis, such asPRSS1, PRSS2, CTRC, SPINK1, CFTR, ALDH2, and CYP2E1. Among the statistically significant markers,D15S1007on chromosome 15q14 showed strong evidence for disease susceptibility (70.8% vs. 35.1%,Pc= 0.0001). Within 500 kb of D15S1007, several genes were candidate genes for susceptibility, includingFMN1, DKFZP686C2281, LOC440268, RYR3, and AVEN, This study identified 10 candidate susceptibility and 5 candidate resistant regions that may contain genes involved in ACP pathogenesis.

scholarly journals Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Sheng-yong Xu ◽  
Na Song ◽  
Shi-jun Xiao ◽  
Tian-xiang Gao
Keyword(s):  
Microsatellite Markers ◽  
Gc Content ◽  
The Philippines ◽  
Whole Genome Sequence ◽  
Northwestern Pacific ◽  
Whole Genome ◽  
Survey Analysis ◽  
Genome Survey ◽  
Sebastiscus Marmoratus ◽  
Wide Range

Abstract The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

scholarly journals Rapid development of 56 novel microsatellite markers for the benthic freshwater bug Aphelocheirus aestivalis using Illumina paired-end sequencing data and M13-tailed primers

2020 ◽  
Vol 47 (12) ◽  
pp. 9995-10003
Author(s):  
Agnieszka Kaczmarczyk-Ziemba
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rapid Development ◽  
Whole Genome ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Two Samples

AbstractThe freshwater true bug Aphelocheirus aestivalis (Aphelocheiridae) is widely distributed in Europe but occurs rather locally and often in isolated populations. Moreover, it is threatened with extinction in parts of its range. Unfortunately, little is known about the genetic diversity and population structure due to the lack of molecular tools for this species. Thus, to overcome the limitations, a whole-genome sequencing has been performed to identify polymorphic microsatellite markers for A. aestivalis. The whole-genome sequencing has been performed with the Illumina MiSeq platform. Obtained paired-end reads were processed and overlapped into 2,378,426 sequences, and the subset of 267 sequences containing microsatellite motifs were then used for in silico primer designing. Finally, 56 microsatellite markers were determined and 34 of them were polymorphic. Analyses performed in two samples (collected from Drawa and Gowienica rivers, respectively) showed that the number of alleles per locus ranged from 2 to 21, and the observed and expected heterozygosity varied from 0 to 0.933 and 0.064 to 0.931, respectively. The microsatellite markers developed in the present study provide new suitable tools available for the scientific community to study A. aestivalis population dynamics. The assessment of its genetic diversity and population structure will provide important data, that can be used in population management and conservation efforts, elucidating the broad- and fine-scale population genetic structure of A. aestivalis.

scholarly journals Looking for breed differentiating SNP loci and for a SNP set for parentage testing in Mangalica

2013 ◽  
Vol 56 (1) ◽  
pp. 200-207 ◽  
Author(s):  
A. Zsolnai ◽  
G. Tóth ◽  
J. Molnár ◽  
V. Stéger ◽  
F. Marincs ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Whole Genome ◽  
Parentage Testing ◽  
Exclusion Probability

Abstract. The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the possibility (1) to replace the previously applied ten microsatellite markers by nine SNP loci to classify the Blond, Swallow-Belly and Red Mangalica individuals into three different breed groups (P>0.95); (2) to propose 54 SNP loci for parentage testing in Mangalica pigs where the exclusion probability is 0.999115 if one parent is known and the probability of identity is 1.54×10-23.

Microsatellite Markers from Whole Genome and Transcriptomic Sequences

2021 ◽  
pp. 387-412
Author(s):  
Manoj Kumar Gupta ◽  
Ravindra Donde ◽  
S. Sabarinathan ◽  
Gayatri Gouda ◽  
Goutam Kumar Dash ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Whole Genome

scholarly journals Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

2015 ◽  
Vol 9 (12) ◽  
pp. e0004316 ◽  
Author(s):  
Mónica J. Pajuelo ◽  
María Eguiluz ◽  
Eric Dahlstrom ◽  
David Requena ◽  
Frank Guzmán ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genome Analysis ◽  
Taenia Solium ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Identification And Characterization

Refining the results of a whole-genome screen based on 4666 microsatellite markers for defining predisposition factors for multiple sclerosis

2004 ◽  
Vol 25 (14) ◽  
pp. 2212-2218 ◽  
Author(s):  
René Gödde ◽  
Viktoria Nigmatova ◽  
Peter Jagiello ◽  
Eckhart Sindern ◽  
Michael Haupts ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Microsatellite Markers ◽  
Whole Genome ◽  
Genome Screen
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