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

Abstract

BackgroundRhodnius 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 findingsThe 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/SignificanceOur 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.

Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species

“…Therefore, AlfI is expected to have a greater density of restriction sites across any genome than CspCI, and potentially yield more loci as observed in the kissing bug Rhodnius ecuadoriensis (Hernandez-Castro et al, 2017).…”

“…Moreover, AlfI provided higher number of loci than CspCI in both species as expected, since AlfI recognition sequence has six fixed nucleotides, while CspCI has seven fixed nucleotides. Therefore, AlfI is expected to have a greater density of restriction sites across any genome than CspCI, and potentially yield more loci as observed in the kissing bug Rhodnius ecuadoriensis (Hernandez‐Castro et al, 2017).…”

Under pressure: phenotypic divergence and convergence associated with microhabitat adaptations in Triatominae

“…The reddish shade in Loja suggests possible, partial differentiation of local populations in the Catamayo-Chira basin, as indicated by the identification of three closely related cytb haplotypes (LJ1–LJ3) not shared with other populations (Figs. 7 , 8 ) and by limited microsatellite [ 41 ] and 2b-RAD (restriction site-associated DNA tag sequencing/genotyping based on type IIB restriction enzymes) genotyping data [ 79 ]. Colored circles show the approximate geographic location (on the map) of cytb haplotypes and their correspondence with each phenotype (on bug pictures); color codes are as in Figs.…”

Under pressure: phenotypic divergence and convergence associated with microhabitat adaptations in Triatominae

“…Below we argue that local adaptation to distinct microhabitats is probably the key driver underpinning this remarkable example of population-level phenotypic diversity. (Fig 7) and by limited microsatellite [67] and 2b-RAD genotyping data [75]. Triatomines are blood-sucking bugs that live in sheltered microhabitats with a more-orless stable food supply [1,2,27].…”