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Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms.
- Source :
-
Molecular Ecology Resources . Mar2014, Vol. 14 Issue 2, p393-400. 8p. - Publication Year :
- 2014
-
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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 1755098X
- Volume :
- 14
- Issue :
- 2
- Database :
- Academic Search Index
- Journal :
- Molecular Ecology Resources
- Publication Type :
- Academic Journal
- Accession number :
- 94514608
- Full Text :
- https://doi.org/10.1111/1755-0998.12179