Data from: Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms
Quillery, Elsa, French National Institute for Agricultural Research
Quenez, Olivier, Inria Rennes - Bretagne Atlantique Research Centre
Peterlongo, Pierre, Inria Rennes - Bretagne Atlantique Research Centre
Plantard, Olivier, French National Institute for Agricultural Research
Published Dec 10, 2013 on Dryad.
Cite this dataset
Quillery, Elsa; Quenez, Olivier; Peterlongo, Pierre; Plantard, Olivier (2013). Data from: Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms [Dataset]. Dryad. https://doi.org/10.5061/dryad.1h1f2
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.
output data generated by Read2snps tool. This file contain only SNPs sequences with SNPs with a depth sequencing between 4 and 10 for a minimum quality of 30. This file have been used to select and to design primers.