Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms.
Mol Ecol Resour
; 14(2): 393-400, 2014 Mar.
Article
em En
| MEDLINE
| ID: mdl-24119113
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Ixodes
/
Polimorfismo de Nucleotídeo Único
/
Genômica
/
Genética Populacional
Tipo de estudo:
Prognostic_studies
Limite:
Animals
País/Região como assunto:
Europa
Idioma:
En
Ano de publicação:
2014
Tipo de documento:
Article