title: 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.
authors.affiliation: INRA, UMR1300 Biology, Epidemiology and Risk Analysis in animal health, BP 40706, F-44307, Nantes, France; LUNAM Université, Oniris, Ecole nationale vétérinaire, agroalimentaire et de l'alimentation Nantes Atlantique, UMR BioEpAR, Nantes, 44307, France.
authors.forename: E
authors.initials: E
authors.lastname: Quillery
authors.forename: O
authors.initials: O
authors.lastname: Quenez
authors.forename: P
authors.initials: P
authors.lastname: Peterlongo
authors.forename: O
authors.initials: O
authors.lastname: Plantard
mesh_terms: D000818:Animals; D019295:Computational Biology; D005060:Europe; D005828:Genetics, Population / Q000379:methods*; D023281:Genomics / Q000379:methods*; D018884:Ixodes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: 454; Ixodes ricinus; SNP; de novo SNP calling; nonmodel organism; reduced representation library