10.5061/DRYAD.02BF1
Hernandez Castro, Luis Enrique
Paterno, Marta
University of Padua
Villacís, Anita G.
Pontificia Universidad Católica del Ecuador
Andersson, Björn
Karolinska Institute
Costales, Jaime A.
Pontificia Universidad Católica del Ecuador
De Noia, Michele
Bielefeld University
Ocaña-Mayorga, Sofía
Pontificia Universidad Católica del Ecuador
Yumiseva, Cesar A.
Pontificia Universidad Católica del Ecuador
Grijalva, Mario J.
Ohio University
Llewellyn, Martin S.
University of Glasgow
Hernandez-Castro, Luis E.
University of Glasgow
Data from: 2b-RAD genotyping for population genomic studies of Chagas
disease vectors: Rhodnius ecuadoriensis in Ecuador
Dryad
dataset
2018
Vector control
Chagas disease
Rhodnius ecuadoriensis
2b-RAD geotyping
Next Generation Sequencing
2018-06-29T00:00:00Z
2018-06-29T00:00:00Z
en
https://doi.org/10.1371/journal.pntd.0005710
502879881 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
2b-RAD raw data of Rhodnius ecuadoriensisSequencing A) Clustering was done
by ‘onboard clustering’ and samples were sequenced on MiSeq (MSC
2.5.0.5/RTA 1.18.54) with a 1x51 setup using ‘Version2’ chemistry. The Bcl
to FastQ conversion was performed using bcl2fastq-1.8.4 from the CASAVA
software suite. The quality scale used is Sanger / phred33 / Illumina
1.8+.2bRADseq_Recuadoriensis.zip
Manabi
Ecuador
Loja