2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.
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 consi...
Published in: | PLOS Neglected Tropical Diseases |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2017
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pntd.0005710 https://doaj.org/article/36938f26430d4b8280974208c4227ac6 |
id |
ftdoajarticles:oai:doaj.org/article:36938f26430d4b8280974208c4227ac6 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:36938f26430d4b8280974208c4227ac6 2023-05-15T15:12:34+02:00 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. Luis E Hernandez-Castro Marta Paterno Anita G Villacís Björn Andersson Jaime A Costales Michele De Noia Sofía Ocaña-Mayorga Cesar A Yumiseva Mario J Grijalva Martin S Llewellyn 2017-07-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0005710 https://doaj.org/article/36938f26430d4b8280974208c4227ac6 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC5536387?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0005710 https://doaj.org/article/36938f26430d4b8280974208c4227ac6 PLoS Neglected Tropical Diseases, Vol 11, Iss 7, p e0005710 (2017) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2017 ftdoajarticles https://doi.org/10.1371/journal.pntd.0005710 2022-12-31T13:06:11Z 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.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.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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 11 7 e0005710 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Luis E Hernandez-Castro Marta Paterno Anita G Villacís Björn Andersson Jaime A Costales Michele De Noia Sofía Ocaña-Mayorga Cesar A Yumiseva Mario J Grijalva Martin S Llewellyn 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
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.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.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. |
format |
Article in Journal/Newspaper |
author |
Luis E Hernandez-Castro Marta Paterno Anita G Villacís Björn Andersson Jaime A Costales Michele De Noia Sofía Ocaña-Mayorga Cesar A Yumiseva Mario J Grijalva Martin S Llewellyn |
author_facet |
Luis E Hernandez-Castro Marta Paterno Anita G Villacís Björn Andersson Jaime A Costales Michele De Noia Sofía Ocaña-Mayorga Cesar A Yumiseva Mario J Grijalva Martin S Llewellyn |
author_sort |
Luis E Hernandez-Castro |
title |
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. |
title_short |
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. |
title_full |
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. |
title_fullStr |
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. |
title_full_unstemmed |
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. |
title_sort |
2b-rad genotyping for population genomic studies of chagas disease vectors: rhodnius ecuadoriensis in ecuador. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2017 |
url |
https://doi.org/10.1371/journal.pntd.0005710 https://doaj.org/article/36938f26430d4b8280974208c4227ac6 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 11, Iss 7, p e0005710 (2017) |
op_relation |
http://europepmc.org/articles/PMC5536387?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0005710 https://doaj.org/article/36938f26430d4b8280974208c4227ac6 |
op_doi |
https://doi.org/10.1371/journal.pntd.0005710 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
11 |
container_issue |
7 |
container_start_page |
e0005710 |
_version_ |
1766343233523154944 |