Abstract
BackgroundGenetic markers are widely used to understand the biology and population dynamics of disease vectors, but often markers are limited in the resolution they provide. In particular, the delineation of population structure, fine scale movement and patterns of relatedness are often obscured unless numerous markers are available. To address this issue in the major arbovirus vector, the yellow fever mosquito (Aedes aegypti), we used double digest Restriction-site Associated DNA (ddRAD) sequencing for the discovery of genome-wide single nucleotide polymorphisms (SNPs). We aimed to characterize the new SNP set and to test the resolution against previously described microsatellite markers in detecting broad and fine-scale genetic patterns in Ae. aegypti.ResultsWe developed bioinformatics tools that support the customization of restriction enzyme-based protocols for SNP discovery. We showed that our approach for RAD library construction achieves unbiased genome representation that reflects true evolutionary processes. In Ae. aegypti samples from three continents we identified more than 18,000 putative SNPs. They were widely distributed across the three Ae. aegypti chromosomes, with 47.9% found in intergenic regions and 17.8% in exons of over 2,300 genes. Pattern of their imputed effects in ORFs and UTRs were consistent with those found in a recent transcriptome study. We demonstrated that individual mosquitoes from Indonesia, Australia, Vietnam and Brazil can be assigned with a very high degree of confidence to their region of origin using a large SNP panel. We also showed that familial relatedness of samples from a 0.4 km2 area could be confidently established with a subset of SNPs.ConclusionsUsing a cost-effective customized RAD sequencing approach supported by our bioinformatics tools, we characterized over 18,000 SNPs in field samples of the dengue fever mosquito Ae. aegypti. The variants were annotated and positioned onto the three Ae. aegypti chromosomes. The new SNP set provided much greater resolution in detecting population structure and estimating fine-scale relatedness than a set of polymorphic microsatellites. RAD-based markers demonstrate great potential to advance our understanding of mosquito population processes, critical for implementing new control measures against this major disease vector.
Highlights
Genetic markers are widely used to understand the biology and population dynamics of disease vectors, but often markers are limited in the resolution they provide
We demonstrated the high potential of genome-wide single nucleotide polymorphisms (SNPs) markers to advance our understanding of mosquito population dynamics which is crucial for improving the control measures against this major disease vector
Bioinformatics tools: DDsilico and DDemux We developed DDsilico as a memory efficient program written in C language for in silico genome digestion with a single restriction enzyme or a combination of enzymes
Summary
Genetic markers are widely used to understand the biology and population dynamics of disease vectors, but often markers are limited in the resolution they provide. The delineation of population structure, fine scale movement and patterns of relatedness are often obscured unless numerous markers are available. To address this issue in the major arbovirus vector, the yellow fever mosquito (Aedes aegypti), we used double digest Restriction-site Associated DNA (ddRAD) sequencing for the discovery of genome-wide single nucleotide polymorphisms (SNPs). Close association with repetitive genetic elements and lower polymorphism has hindered the development of a robust set of microsatellite markers in Ae. aegypti until the complete genome sequence became available [10,11,12]. Population genetic structure of this vector has since been usually ascertained with up to 12 microsatellite loci [13], that were sometimes supplemented with a few single nucleotide polymorphism (SNP) markers [14] or ExonPrimed Intron Crossing (EPIC) markers [15,16,17]
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