Rašić Gordana, Filipović Igor, Weeks Andrew R, Hoffmann Ary A
Pest and Disease Vector Group, Department of Genetics, The University of Melbourne, Victoria 3010, Australia.
BMC Genomics. 2014 Apr 11;15:275. doi: 10.1186/1471-2164-15-275.
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. 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.
We 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.
Using 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.
遗传标记被广泛用于了解病媒生物的生物学特性和种群动态，但通常这些标记所提供的分辨率有限。特别是，除非有大量标记，否则种群结构、精细尺度的移动以及亲缘关系模式往往难以明确。为了解决主要虫媒病毒病媒埃及伊蚊中的这一问题，我们使用双酶切限制性位点关联DNA（ddRAD）测序来发现全基因组单核苷酸多态性（SNP）。我们旨在对新的SNP集进行特征描述，并在检测埃及伊蚊广泛和精细尺度的遗传模式时，将其分辨率与先前描述的微卫星标记进行比较。
我们开发了生物信息学工具，支持针对SNP发现定制基于限制性内切酶的方案。我们表明，我们构建RAD文库的方法实现了无偏倚的基因组代表性，反映了真实的进化过程。在来自三大洲的埃及伊蚊样本中，我们鉴定出了超过18000个推定的SNP。它们广泛分布在埃及伊蚊的三条染色体上，47.9%位于基因间区域，17.8%位于2300多个基因的外显子中。它们在开放阅读框和非翻译区的推定效应模式与最近的转录组研究结果一致。我们证明，使用一个大型SNP面板，可以非常高的置信度将来自印度尼西亚、澳大利亚、越南和巴西的单个蚊子归属于它们的起源地区。我们还表明，使用SNP子集可以可靠地确定来自0.4平方公里区域样本的家族亲缘关系。
使用由我们的生物信息学工具支持的经济高效的定制RAD测序方法，我们对登革热媒介埃及伊蚊的野外样本中的18000多个SNP进行了特征描述。这些变异被注释并定位到埃及伊蚊的三条染色体上。与一组多态性微卫星相比，新的SNP集在检测种群结构和估计精细尺度亲缘关系方面提供了更高的分辨率。基于RAD的标记显示出巨大潜力，可推进我们对蚊种种群过程的理解，这对于实施针对这种主要病媒的新控制措施至关重要。
