Isolation and characterisation of microsatellites for the endangered Slater’s skink, Liopholis slateri (Squamata : Scincidae), via next-generation sequencing

2017 ◽  
Vol 65 (3) ◽  
pp. 200 ◽  
Author(s):  
Michael G. Gardner ◽  
Mina H. Ansari ◽  
Claire E. Treilibs ◽  
Angharad Johnston ◽  
Chris R. Pavey ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Next Generation Sequencing ◽  
Microsatellite Loci ◽  
Shotgun Sequencing ◽  
Next Generation ◽  
Central Australia ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

We characterised 14 new polymorphic microsatellite loci for the endangered lizard Liopholis slateri. Initially, 454 shotgun sequencing was used to identify 46 loci, which were trialled for amplification. Subsequently, 14 of these loci were screened for variation in 21 individuals from scat-derived DNA samples collected from Owen Springs Reserve in central Australia. All 14 loci were polymorphic, with observed heterozygosity ranging from 0.19 to 0.86 and the number of alleles per locus ranging from 2 to 10. These loci will be useful in understanding the genetic variation and connectivity within and among extant L. slateri populations.

Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing

2012 ◽  
Vol 4 (3) ◽  
pp. 811-814 ◽  
Author(s):  
Yoshimi Shinmura ◽  
Alison K. S. Wee ◽  
Koji Takayama ◽  
Takeshi Asakawa ◽  
Orlex Baylen Yllano ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Loci ◽  
Next Generation ◽  
Sonneratia Alba ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

Polymorphic microsatellite loci and partial mitogenome for the Chestnut-bellied Seed-finch Sporophila angolensis (Aves, Passeriformes) using next generation sequencing

2019 ◽  
Vol 46 (4) ◽  
pp. 4617-4623 ◽  
Author(s):  
Cássia Alves Lima-Rezende ◽  
Sarah Dobkowski-Marinho ◽  
Gislaine Aparecida Fernandes ◽  
Fernando Pacheco Rodrigues ◽  
Renato Caparroz
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Loci ◽  
Next Generation ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

Development of nineteen polymorphic microsatellite loci in the threatened polar bear (Ursus maritimus) using next generation sequencing

2013 ◽  
Vol 6 (1) ◽  
pp. 59-61 ◽  
Author(s):  
Jessica R. Brandt ◽  
Peter J. Van Coeverden de Groot ◽  
Kai Zhao ◽  
Markus G. Dyck ◽  
Peter T. Boag ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Loci ◽  
Polar Bear ◽  
Ursus Maritimus ◽  
Next Generation ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

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.

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