Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in HaitiReportar como inadecuado

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BMC Genomics

, 10:590

First Online: 09 December 2009Received: 16 July 2009Accepted: 09 December 2009


BackgroundMicrosatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti.

ResultsFrom 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority 51% of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus mean = 8.75. Allelic polymorphic information content varied from 0.171 to 0.867 mean = 0.545. Most loci met Hardy-Weinberg expectations across populations and pairwise FST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed.

ConclusionDespite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient screening of genome supercontig assemblies. These loci are suitable for genetic and population studies using multiplex-PCR.

AbbreviationsTRFTandem Repeats Finder

wgswhole genome sequence

PICpolymorphic information content


Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-10-590 contains supplementary material, which is available to authorized users.

Diane D Lovin, Katie O Washington contributed equally to this work.

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Autor: Diane D Lovin - Katie O Washington - Becky deBruyn - Ryan R Hemme - Akio Mori - Sarah R Epstein - Brent W Harker - Tho


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