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PLoS Negl Trop Dis. 2017 Jul 19;11(7):e0005710. doi: 10.1371/journal.pntd.0005710. eCollection 2017 Jul.

2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.

Author information

1
Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom.
2
Department of Biology, University of Padua, Padua, Italy.
3
Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.
4
Center for Research on Health in Latin America, School of Biological Sciences, Pontifical Catholic University of Ecuador, Quito, Ecuador.
5
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
6
Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.
7
Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Ohio, United States of America.

Abstract

BACKGROUND:

Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses.

METHODOLOGY/PRINCIPAL FINDINGS:

The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area.

CONCLUSIONS/SIGNIFICANCE:

Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment.

PMID:
28723901
PMCID:
PMC5536387
DOI:
10.1371/journal.pntd.0005710
[Indexed for MEDLINE]
Free PMC Article

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