Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti

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.

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

“…The relatively high transition/transversion ratio of 2.04 after filtering for paralogs and mitochondrial loci may indicate a bias toward genic regions, as SNPs occur more frequently as transitions in exons than in introns (Park, Yu, Mun, & Lee, 2010). This value may also reflect effective filters to reduce sequencing error in the final SNP dataset (Pujolar et al., 2013; Rašić, Filipović, Weeks, & Hoffmann, 2014; Zhang et al., 2015). Initial examination of the SNP data, prior to filtering, showed many SNPs in the last few base pairs of reads (Figure S2) that may reflect sequencing errors rather than true variants (Pujolar et al., 2013).…”

Insecticide resistance and genetic variability in natural populations of Aedes (Stegomyia) aegypti (Diptera: Culicidae) from Colombia

“…The current trend is to use microsatellites (MONTEIRO et al 2014) and/or SNPs (single nucleotide polymorphism) (RASIC et al 2014). Nevertheless, mitochondrial DNA (mtDNA) has been widely used in population genetics studies of A. aegypti from different geographic points and dengue endemic regions (GONÇALVES et al 2012).…”

How much is known about the genetic diversity of the Asian tiger mosquito? A systematic review

“…Genetic markers are widely used to understand the biology and population dynamics of disease vectors 87 . However, in our study, the 89.5% of the known genetic diversity is based on the use of RFLP, allozymes, isozymes, and mitochondrial molecular markers, which have problems reported in the literature.…”

“…Despite the mtDNA markers have been widely used in vector genetic diversity studies, including A. albopictus 29,100 , these are not as sensitive to detect genetic variation as microsatellites and/or SNPs (Single Nucleotide Polymorphism) are 61,87 . Microsatellites have been used as genetic markers for a number of arthropod vectors of human diseases, including A. albopictus 32 .…”

“…Currently, SNPs have become one of the selectable markers for studies on population genetics, characterization of genes or disease to elucidate the evolutionary processes at the molecular level, since they are easy to detect when compared, for example, with microsatellites 87,105 . In vectors diseases such as Anopheles gambiae, A. funestus (vectors of malaria in Africa) and A. aegypti, SNPs have been highly polymorphic 87,104,[106][107] . For A. aegypti, Paduan & Ribolla 106 sequenced seven genes of 16 Brazilian populations of this species.…”