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

Abstract

Assessing the genetic variability of the tick Ixodes ricinus-an important vector of pathogens in Europe-is an essential step for setting up antitick control methods. Here, we report the first identification of a set of SNPs isolated from the genome of I. ricinus, by applying a reduction in genomic complexity, pyrosequencing and new bioinformatics tools. Almost 1.4 million of reads (average length: 528 nt) were generated with a full Roche 454 GS FLX run on two reduced representation libraries of I. ricinus. A newly developed bioinformatics tool (DiscoSnp), which isolates SNPs without requiring any reference genome, was used to obtain 321 088 putative SNPs. Stringent selection criteria were applied in a bioinformatics pipeline to select 1768 SNPs for the development of specific primers. Among 384 randomly SNPs tested by Fluidigm genotyping technology on 464 individuals ticks, 368 SNPs loci (96%) exhibited the presence of the two expected alleles. Hardy-Weinberg equilibrium tests conducted on six natural populations of ticks have shown that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiency.

Keywords: 454; Ixodes ricinus; SNP; de novo SNP calling; nonmodel organism; reduced representation library.