Microsatellite markers developed in the stingless bee Melipona fasciculata by next-generation sequencing and an exploratory analysis of geographic genetic variation
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Abstract
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.
Cite this as
2017. Microsatellite markers developed in the stingless bee Melipona fasciculata by next-generation sequencing and an exploratory analysis of geographic genetic variation. PeerJ Preprints 5:e3382v1 https://doi.org/10.7287/peerj.preprints.3382v1Author comment
This is a submission to PeerJ for review.
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Raw data input
Raw data input for analyses in GenAlex and other programs
Additional Information
Competing Interests
The authors declare there are no competing interests.
Author Contributions
Geice R Silva conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables.
Isis G B Souza conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper.
Bruno A Souza contributed reagents/materials/analysis tools.
Fábia M Pereira contributed reagents/materials/analysis tools.
Maria Teresa R Lopes contributed reagents/materials/analysis tools.
Paul Bentzen conceived and designed the experiments, contributed reagents/materials/analysis tools.
Fabio Mendonça Diniz conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
The following information was supplied regarding the deposition of DNA sequences: Gen Bank accession numbers KT730150 - KT730167.
Funding
This work was granted by Embrapa Macroprograma2 (02.11.01.029.00.00) and the Brazilian Federal Government (Science without Borders program) scholarship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
