Data from: Identifying insecticide resistance genes in mosquito by combining AFLP genome scan and 454 pyrosequencing

AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection due to the difficulty to obtain the sequences from AFLP fragments. Here we combine classical AFLP outlier detection to 454 sequencing of AFLP fragments obtained from chosen individuals to obtain the sequence of outliers. We applied this approach to the study of resistance to Bacillus thuringiensis israelensis (Bti) toxins in the dengue vector Aedes aegypti. A genome scan of Bti-resistant and Bti-susceptible Aedes aegypti laboratory strains was performed based on 432 AFLP markers. Fourteen outliers were detected using two different population genetics algorithms, a frequentist and a Bayesian approach. Out of these, 11 were successfully sequenced. Three contained transposable elements (TEs) sequences. The 10 outliers that could be mapped at a unique location in the reference genome were located on different supercontigs, underlying the multigenic basis of resistance to Bti toxins. One outlier was in the vicinity of a gene coding for an aminopeptidase potentially involved in Bti toxin binding. Patterns of sequence variability of this gene showed significant deviation from neutrality in the resistant strain but not in the susceptible strain, even after taking into account the known demographic history of the selected strain. This gene is a promising candidate for future functional analysis.

基于扩增片段长度多态性（Amplified Fragment Length Polymorphism，AFLP）的基因组扫描技术已被广泛应用于适应性遗传学研究，以及潜在受选择作用的基因组区域的鉴定工作。然而，由于难以从AFLP片段中获取序列信息，该方法通常无法检测到选择所靶向的真实基因或突变位点。本研究将经典的AFLP离群位点检测方法，与从选定个体中获取的AFLP片段的454测序（454 sequencing）相结合，以获取离群位点的序列信息。我们将该方法应用于登革热传播媒介埃及伊蚊（Aedes aegypti）对苏云金杆菌以色列亚种（Bacillus thuringiensis israelensis，Bti）毒素的抗性研究。研究基于432个AFLP标记，对Bti抗性与Bti敏感的埃及伊蚊实验室品系开展了基因组扫描。通过两种不同的群体遗传学算法——频率学派（frequentist）方法与贝叶斯学派（Bayesian）方法——共检测到14个离群位点。其中11个离群位点成功完成测序。3个离群位点包含转座因子（transposable elements，TEs）序列。可在参考基因组中定位到唯一位置的10个离群位点分布于不同的超级重叠群（supercontig）上，这揭示了Bti毒素抗性的多基因遗传基础。1个离群位点位于一个编码氨肽酶（aminopeptidase）的基因附近，该氨肽酶可能参与Bti毒素的结合过程。对该基因的序列变异模式分析显示，在抗性品系中其变异模式显著偏离中性进化，但在敏感品系中未出现此现象；即便在考虑了所选品系已知的种群历史后，该结果依然成立。该基因有望成为未来功能分析的潜在候选基因。