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

Elsa Quillery 1, * Olivier Quenez 2, 3 Pierre Peterlongo 4 Olivier Plantard 1
* Corresponding author
1 UMR1300 Biology, Epidemiology and Risk Analysis in animal health
ONIRIS - Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique
2 Plateforme bioinformatique GenOuest [Rennes]
IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE, UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique
3 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
4 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE, Inria Rennes – Bretagne Atlantique
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.
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https://hal.inria.fr/hal-00880072
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Submitted on : Tuesday, November 5, 2013 - 12:29:05 PM
Last modification on : Monday, November 22, 2021 - 1:52:23 PM

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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, Wiley/Blackwell, 2013, 14 (2), pp.393-400. ⟨10.1111/1755-0998.12179⟩. ⟨hal-00880072⟩

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