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Journal Articles Molecular Ecology Resources Year : 2013

Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms

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Abstract

: 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, by applying a reduction of 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 (Read2Snps), 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 1,768 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 6 natural populations of ticks have shown that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiency. This article is protected by copyright. All rights reserved.

Dates and versions

hal-00880072 , version 1 (05-11-2013)

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Elsa Quillery, Olivier Quenez, Pierre Peterlongo, Olivier Plantard. Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms. Molecular Ecology Resources, 2013, 14 (2), pp.393-400. ⟨10.1111/1755-0998.12179⟩. ⟨hal-00880072⟩
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