Data from: Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms

Assessing the genetic variability of the tick Ixodes ricinus - an important vector of pathogens in Europe - is an essential step for setting-up anti-tick control methods. Here, we report the first identification of a set of SNPs isolated from the genome of I. ricinus, carried out by applying a genomic complexity reduction step, followed by pyrosequencing and the use new bioinformatics tools. Almost 1.4 million reads (average length : 528 nt) were generated with a full Roche 454 GS FLX run on two Reduced Representation Libraries of I. ricinus. 321,088 putative SNPs were isolated using the newly developed bioinformatics tool READ2SNPS, which identifies SNPs without requiring a reference genome. Stringent selection criteria were applied in a bioinformatics pipeline to select 1,768 SNPs for the development of specific primers. Among 384 randomly selected SNPs, tested by Fluidigm genotyping technology on 464 individual ticks, 368 SNPs loci (96%) exhibited the presence of the two expected alleles. Hardy-Weinberg equilibrium tests conducted on 6 natural populations of ticks showed that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiencies. The generated SNP resource described here will be useful for a variety of applications such as the assessment of the genetic structure of I. ricinus populations.

评估蜱虫物种蓖麻硬蜱（Ixodes ricinus）——欧洲重要的病原体传播媒介——的遗传变异，是建立蜱虫防控策略的核心前提。本研究首次报道从蓖麻硬蜱基因组中分离得到的一组单核苷酸多态性（Single Nucleotide Polymorphisms，简称SNPs），该工作通过基因组复杂度降低步骤、焦磷酸测序以及新型生物信息学工具完成。本研究针对蓖麻硬蜱的两个简化基因组文库（Reduced Representation Libraries）开展全流程罗氏454 GS FLX测序，共获得近140万条读长序列（平均长度528 nt）。借助新开发的生物信息学工具READ2SNPS（无需参考基因组即可识别SNPs），本研究共筛选得到321088个推定SNPs。通过生物信息学分析流程中的严格筛选标准，最终选取1768个SNPs用于特异性引物开发。从随机选取的384个SNPs中，采用Fluidigm基因分型技术对464只单个蜱虫进行分型检测，其中368个SNP位点（占比96%）成功扩增出预期的两种等位基因。对6个蜱虫自然种群开展哈迪-温伯格平衡检验（Hardy-Weinberg equilibrium），结果显示384个位点中有26至46个位点表现出显著的杂合子缺失现象。本研究构建的SNP资源可应用于多项研究场景，例如评估蓖麻硬蜱种群的遗传结构。