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 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 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 of microsatellite markers from genomic DNA of Parashorea malaanonan (Dipterocarpaceae) using next-generation sequencing

2019 ◽  
Vol 68 (1) ◽  
pp. 22-25 ◽  
Author(s):  
Crusty E. Tinio ◽  
Saneyoshi Ueno ◽  
Kentaro Uchiyama ◽  
Lerma S. J. Maldia ◽  
Nobuhiro Tomaru
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Genomic Dna ◽  
Molecular Ecology ◽  
Pcr Amplification ◽  
The Philippines ◽  
Next Generation ◽  
Adult Trees ◽  
High Level ◽  
Generation Sequencing

Abstract Twenty polymorphic microsatellite markers were developed, using Next Generation Sequencing (Illumina), from genomic DNA of Parashorea malaanonan, a species of the Dipterocarpa­ceae which is ecologically and economically important in the Philippines. Thirty adult trees from a natural population were used to assess the success of PCR amplification and the degree of polymorphism. The number of alleles per locus varied from three to 13, and observed and expected heterozygosity varied from 0.200 to 0.808 and from 0.301 to 0.890 respectively. Total exclusion probabilities for the first and second parents over the 20 loci were 0.99932499 and 0.99999723 respectively. The high level of polymorphism at these loci makes it possible to obtain precise estimates of genetic parameters and thus the markers will help in studies on population genetics, conservation gene­tics, and molecular ecology of P. malaanonan.

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

scholarly journals Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

BMC Ecology ◽  
2013 ◽  
Vol 13 (1) ◽  
pp. 8 ◽  
Author(s):  
Hannah McPherson ◽  
Marlien van der Merwe ◽  
Sven K Delaney ◽  
Mark A Edwards ◽  
Robert J Henry ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Ecology ◽  
Next Generation ◽  
Generation Sequencing
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