16 microsatellite loci for the Australian Great Artesian Basin spring amphipod, Wangiannachiltonia guzikae

2013 ◽  
Vol 61 (2) ◽  
pp. 109 ◽  
Author(s):  
Hannah L. Robertson ◽  
Nicholas P. Murphy
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Single Population ◽  
Artesian Basin ◽  
Great Artesian Basin ◽  
Hardy Weinberg Equilibrium ◽  
Stochastic Events ◽  
Generation Sequencing ◽  
454 Next Generation Sequencing

454 Next Generation sequencing was used to develop a set of microsatellite markers for the Great Artesian Basin (GAB) amphipod, Wangiannachiltonia guzikae. Primers were designed for 42 microsatellite loci. A total of 22 loci were successfully amplified and 16 characterised using 30 individuals from a single GAB spring population. Across these 16 loci, observed heterozygosity ranged from 0.000 to 0.818 (mean = 0.445) and the number of alleles per locus ranged from 2 to 12 (mean = 6.688). Of these 16 loci, however, only 10 were in Hardy–Weinberg equilibrium, though all 16 loci should be retained for further studies in the event that stochastic events affected equilibrium of this single population.

scholarly journals Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2019 ◽  
Author(s):  
Christine Ewers-Saucedo ◽  
John D. Zardus ◽  
John P. Wares
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Next Generation Sequencing Data ◽  
Model Organisms ◽  
Next Generation ◽  
Sequencing Data ◽  
Genetic Studies ◽  
Evolutionary Features ◽  
Generation Sequencing

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758).Chelonibia testudinariaappears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies onC. testudinaria.

scholarly journals Development of microsatellite markers using 454 sequencing for the rare socially parasitic hoverfly, Microdon mutabilis

2012 ◽  
Vol 60 (2) ◽  
pp. 108
Author(s):  
Juergen von Zum Hof ◽  
Karsten Schönrogge ◽  
James M. Cook ◽  
Michael G. Gardner
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Molecular Ecology ◽  
454 Sequencing ◽  
Polymorphic Markers ◽  
Fine Scale ◽  
Next Generation ◽  
Generation Sequencing

To date there have been only limited fine-scale investigations into the molecular ecology of the European hoverfly, Microdon mutabilis, due to the paucity of available polymorphic markers. We describe the development of primers amplifying five novel microsatellite loci using next-generation sequencing (454) and three previously undescribed M. mutabilis microsatellite loci using enrichments. In hoverflies from a population in Ireland, the number of alleles per locus ranged from 2 to 16, and the observed heterozygosity ranged between 0.26 and 0.97

scholarly journals Microsatellite markers developed in the stingless bee Melipona fasciculata by next-generation sequencing and an exploratory analysis of geographic genetic variation

2017 ◽  
Author(s):  
Geice R Silva ◽  
Isis G B Souza ◽  
Bruno A Souza ◽  
Fábia M Pereira ◽  
Maria Teresa R Lopes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Differentiation ◽  
Sequence Data ◽  
Exploratory Analysis ◽  
Next Generation ◽  
Generation Sequencing

Background. Native meliponines are currently threatened by increased human impacts. The assessment of their genetic variation by microsatellite DNA markers can assist in the conservation of populations and help in the planning and establishment of efficient management strategies. Next generation sequencing has proven to be useful for identifying microsatellite loci from the large amounts of sequence data generated. Methods. The purpose of this study was to develop the first set of microsatellite markers for Melipona fasciculata, selected from partial genome assembly of Illumina paired-end reads. Contigs were created from the resulting paired-end sequence data and these were analyzed with specialized software to extract those reads that contained microsatellite loci. Primer pairs were designed for each detected locus at their flanking regions. Bee samples were genotyped from two different locations for markers characterization and validation. Results. A total of 17 microsatellite loci displayed polymorphism from two different populations of Northeastern Brazil. Mean HE and HO heterozygosities were 0.453 and 0.536, respectively. PIC across all loci ranged from 0.108 to 0.714. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.194, RST = 0.230, and Dest = 0.162). PCoA and Bayesian clustering showed a separation of the species into two distinct clusters. Discussion. The Illumina paired-end sequencing system provided a large number of microsatellite loci from the M. fasciculata genome. From the genotyped data this study was able to reveal high FST and RST estimates and suggest the existence of genetic structure. These microsatellite markers have demonstrated strong potential for population-level genetic studies and can be used effectively as a molecular tool. Moreover, the exploratory analysis of the genetic diversity in M. fasciculata provides provisional evidence of significant population differentiation between the two studied populations.

scholarly journals Microsatellite markers developed in the stingless bee Melipona fasciculata by next-generation sequencing and an exploratory analysis of geographic genetic variation

2017 ◽  
Author(s):  
Geice R Silva ◽  
Isis G B Souza ◽  
Bruno A Souza ◽  
Fábia M Pereira ◽  
Maria Teresa R Lopes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Differentiation ◽  
Sequence Data ◽  
Exploratory Analysis ◽  
Next Generation ◽  
Generation Sequencing

Background. Native meliponines are currently threatened by increased human impacts. The assessment of their genetic variation by microsatellite DNA markers can assist in the conservation of populations and help in the planning and establishment of efficient management strategies. Next generation sequencing has proven to be useful for identifying microsatellite loci from the large amounts of sequence data generated. Methods. The purpose of this study was to develop the first set of microsatellite markers for Melipona fasciculata, selected from partial genome assembly of Illumina paired-end reads. Contigs were created from the resulting paired-end sequence data and these were analyzed with specialized software to extract those reads that contained microsatellite loci. Primer pairs were designed for each detected locus at their flanking regions. Bee samples were genotyped from two different locations for markers characterization and validation. Results. A total of 17 microsatellite loci displayed polymorphism from two different populations of Northeastern Brazil. Mean HE and HO heterozygosities were 0.453 and 0.536, respectively. PIC across all loci ranged from 0.108 to 0.714. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.194, RST = 0.230, and Dest = 0.162). PCoA and Bayesian clustering showed a separation of the species into two distinct clusters. Discussion. The Illumina paired-end sequencing system provided a large number of microsatellite loci from the M. fasciculata genome. From the genotyped data this study was able to reveal high FST and RST estimates and suggest the existence of genetic structure. These microsatellite markers have demonstrated strong potential for population-level genetic studies and can be used effectively as a molecular tool. Moreover, the exploratory analysis of the genetic diversity in M. fasciculata provides provisional evidence of significant population differentiation between the two studied populations.

scholarly journals Development and Characterization of 68 Microsatellite Markers of Black Amur Bream Megalobrama terminalis by Next-Generation Sequencing

2021 ◽  
Vol 21 (06) ◽  
pp. 299-308
Author(s):  
Kai Liu ◽  
Xiao-yu Feng ◽  
Heng-jia Ma ◽  
Nan Xie
Keyword(s):  
Linkage Disequilibrium ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Polymorphism Information Content ◽  
Next Generation ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

This study developed and characterized 68 novel polymorphic microsatellite markers from black Amur bream Megalobrama terminalis by next-generation sequencing. Variability was tested on 36 individuals collected from Qiantang River, Zhejiang Province, China. The number of alleles per locus ranged from 2 to 13. Observed heterozygosity ranged from 0.028 to 0.944, whereas the expected heterozygosity ranged from 0.028 to 0.887. Polymorphism Information Content ranged from 0.027 to 0.862. Moreover, 53 microsatellites were in agreement with Hardy–Weinberg equilibrium. Twenty-eight pairwise tests in 33 microsatellite loci indicated linkage disequilibrium. These microsatellites are a valuable tool for further genetics studies of this species.

Search for More Effective Microsatellite Markers for Forensics With Next-Generation Sequencing

2017 ◽  
Vol 16 (5) ◽  
pp. 375-381
Author(s):  
Bowen Tan ◽  
Zicheng Zhao ◽  
Zhe Zhang ◽  
Shengbin Li ◽  
Shuai Cheng Li
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Next Generation ◽  
Generation Sequencing
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