Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data

Autores
Gómez Palacio, Andrés; Morinaga, Gen; Turner, Paul E.; Micieli, Maria Victoria; Elnour, Mohammed Ahmed B.; Salim, Bashir; Surendran, Sinnathamby Noble; Ramasamy, Ranjan; Powell, Jeffrey R.; Soghigian, John; Gloria Soria, Andrea
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people worldwide. Population genetic studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasiveranges (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low-coverage whole-genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases,opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole-genome sequencing for population genetic studies of A. aegypti that do not rely on full allelic frequency spectra.Whole-genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.
Fil: Gómez Palacio, Andrés. Universidad Pedagógica y Tecnológica de Colombia; Colombia
Fil: Morinaga, Gen. University of Calgary; Canadá
Fil: Turner, Paul E.. University of Yale; Estados Unidos
Fil: Micieli, Maria Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Estudios Parasitológicos y de Vectores. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Centro de Estudios Parasitológicos y de Vectores; Argentina
Fil: Elnour, Mohammed Ahmed B.. Tropical Medicine Research Institute; Sudán
Fil: Salim, Bashir. University of Khartoum; Sudán
Fil: Surendran, Sinnathamby Noble. University of Jaffna; Sri Lanka
Fil: Ramasamy, Ranjan. University of Jaffna; Sri Lanka
Fil: Powell, Jeffrey R.. University of Yale; Estados Unidos
Fil: Soghigian, John. University of Calgary; Canadá
Fil: Gloria Soria, Andrea. Universidad Pedagógica y Tecnológica de Colombia; Colombia
Materia
genotyping array
SNP chip
Aedes aegypti
population structure
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/267319
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/267319
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing dataGómez Palacio, AndrésMorinaga, GenTurner, Paul E.Micieli, Maria VictoriaElnour, Mohammed Ahmed B.Salim, BashirSurendran, Sinnathamby NobleRamasamy, RanjanPowell, Jeffrey R.Soghigian, JohnGloria Soria, Andreagenotyping arraySNP chipAedes aegyptipopulation structurehttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people worldwide. Population genetic studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasiveranges (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low-coverage whole-genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases,opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole-genome sequencing for population genetic studies of A. aegypti that do not rely on full allelic frequency spectra.Whole-genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.Fil: Gómez Palacio, Andrés. Universidad Pedagógica y Tecnológica de Colombia; ColombiaFil: Morinaga, Gen. University of Calgary; CanadáFil: Turner, Paul E.. University of Yale; Estados UnidosFil: Micieli, Maria Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Estudios Parasitológicos y de Vectores. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Centro de Estudios Parasitológicos y de Vectores; ArgentinaFil: Elnour, Mohammed Ahmed B.. Tropical Medicine Research Institute; SudánFil: Salim, Bashir. University of Khartoum; SudánFil: Surendran, Sinnathamby Noble. University of Jaffna; Sri LankaFil: Ramasamy, Ranjan. University of Jaffna; Sri LankaFil: Powell, Jeffrey R.. University of Yale; Estados UnidosFil: Soghigian, John. University of Calgary; CanadáFil: Gloria Soria, Andrea. Universidad Pedagógica y Tecnológica de Colombia; ColombiaOxford University Press2024-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/267319Gómez Palacio, Andrés; Morinaga, Gen; Turner, Paul E.; Micieli, Maria Victoria; Elnour, Mohammed Ahmed B.; et al.; Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data; Oxford University Press; G3: Genes, Genomes, Genetics; 14; 6; 4-2024; 1-122160-1836CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae082/7646798info:eu-repo/semantics/altIdentifier/doi/10.1093/g3journal/jkae082info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:39:06Zoai:ri.conicet.gov.ar:11336/267319instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:39:06.676CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
title Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
spellingShingle Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
Gómez Palacio, Andrés
genotyping array
SNP chip
Aedes aegypti
population structure
title_short Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
title_full Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
title_fullStr Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
title_full_unstemmed Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
title_sort Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data
dc.creator.none.fl_str_mv Gómez Palacio, Andrés
Morinaga, Gen
Turner, Paul E.
Micieli, Maria Victoria
Elnour, Mohammed Ahmed B.
Salim, Bashir
Surendran, Sinnathamby Noble
Ramasamy, Ranjan
Powell, Jeffrey R.
Soghigian, John
Gloria Soria, Andrea
author Gómez Palacio, Andrés
author_facet Gómez Palacio, Andrés
Morinaga, Gen
Turner, Paul E.
Micieli, Maria Victoria
Elnour, Mohammed Ahmed B.
Salim, Bashir
Surendran, Sinnathamby Noble
Ramasamy, Ranjan
Powell, Jeffrey R.
Soghigian, John
Gloria Soria, Andrea
author_role author
author2 Morinaga, Gen
Turner, Paul E.
Micieli, Maria Victoria
Elnour, Mohammed Ahmed B.
Salim, Bashir
Surendran, Sinnathamby Noble
Ramasamy, Ranjan
Powell, Jeffrey R.
Soghigian, John
Gloria Soria, Andrea
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv genotyping array
SNP chip
Aedes aegypti
population structure
topic genotyping array
SNP chip
Aedes aegypti
population structure
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people worldwide. Population genetic studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasiveranges (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low-coverage whole-genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases,opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole-genome sequencing for population genetic studies of A. aegypti that do not rely on full allelic frequency spectra.Whole-genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.
Fil: Gómez Palacio, Andrés. Universidad Pedagógica y Tecnológica de Colombia; Colombia
Fil: Morinaga, Gen. University of Calgary; Canadá
Fil: Turner, Paul E.. University of Yale; Estados Unidos
Fil: Micieli, Maria Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Estudios Parasitológicos y de Vectores. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Centro de Estudios Parasitológicos y de Vectores; Argentina
Fil: Elnour, Mohammed Ahmed B.. Tropical Medicine Research Institute; Sudán
Fil: Salim, Bashir. University of Khartoum; Sudán
Fil: Surendran, Sinnathamby Noble. University of Jaffna; Sri Lanka
Fil: Ramasamy, Ranjan. University of Jaffna; Sri Lanka
Fil: Powell, Jeffrey R.. University of Yale; Estados Unidos
Fil: Soghigian, John. University of Calgary; Canadá
Fil: Gloria Soria, Andrea. Universidad Pedagógica y Tecnológica de Colombia; Colombia
description The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people worldwide. Population genetic studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasiveranges (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low-coverage whole-genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases,opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole-genome sequencing for population genetic studies of A. aegypti that do not rely on full allelic frequency spectra.Whole-genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.
publishDate 2024
dc.date.none.fl_str_mv 2024-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/267319
Gómez Palacio, Andrés; Morinaga, Gen; Turner, Paul E.; Micieli, Maria Victoria; Elnour, Mohammed Ahmed B.; et al.; Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data; Oxford University Press; G3: Genes, Genomes, Genetics; 14; 6; 4-2024; 1-12
2160-1836
CONICET Digital
CONICET
url http://hdl.handle.net/11336/267319
identifier_str_mv Gómez Palacio, Andrés; Morinaga, Gen; Turner, Paul E.; Micieli, Maria Victoria; Elnour, Mohammed Ahmed B.; et al.; Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data; Oxford University Press; G3: Genes, Genomes, Genetics; 14; 6; 4-2024; 1-12
2160-1836
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae082/7646798
info:eu-repo/semantics/altIdentifier/doi/10.1093/g3journal/jkae082
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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