Improved species assignments across the entire Anopheles genus using targeted sequencing
Issued Date
2024-01-01
Resource Type
eISSN
16648021
Scopus ID
2-s2.0-85205846505
Journal Title
Frontiers in Genetics
Volume
15
Rights Holder(s)
SCOPUS
Bibliographic Citation
Frontiers in Genetics Vol.15 (2024)
Suggested Citation
Boddé M., Makunin A., Teltscher F., Akorli J., Andoh N.E., Bei A., Chaumeau V., Desamours I., Ekpo U.F., Govella N.J., Kayondo J., Kobylinski K., Ngom E.M., Niang E.H.A., Okumu F., Omitola O.O., Ponlawat A., Rakotomanga M.N., Rasolonjatovoniaina M.T., Ayala D., Lawniczak M. Improved species assignments across the entire Anopheles genus using targeted sequencing. Frontiers in Genetics Vol.15 (2024). doi:10.3389/fgene.2024.1456644 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/101617
Title
Improved species assignments across the entire Anopheles genus using targeted sequencing
Author's Affiliation
Mahidol Oxford Tropical Medicine Research Unit
Maladies Infectieuses et Vecteurs : Écologie, Génétique, Évolution et Contrôle
Institut Pasteur de Madagascar
Noguchi Memorial Institute for Medical Research
Uganda Virus Research Institute
Ifakara Health Institute
Institut Pasteur de Dakar
Université Cheikh Anta Diop de Dakar
University of Cambridge
Armed Forces Research Institute of Medical Sciences, Thailand
Nuffield Department of Medicine
Federal University of Agriculture, Abeokuta
Wellcome Sanger Institute
Yale University
Center for Molecular Biodiversity Research
Maladies Infectieuses et Vecteurs : Écologie, Génétique, Évolution et Contrôle
Institut Pasteur de Madagascar
Noguchi Memorial Institute for Medical Research
Uganda Virus Research Institute
Ifakara Health Institute
Institut Pasteur de Dakar
Université Cheikh Anta Diop de Dakar
University of Cambridge
Armed Forces Research Institute of Medical Sciences, Thailand
Nuffield Department of Medicine
Federal University of Agriculture, Abeokuta
Wellcome Sanger Institute
Yale University
Center for Molecular Biodiversity Research
Corresponding Author(s)
Other Contributor(s)
Abstract
Accurate species identification of the mosquitoes in the genus Anopheles is of crucial importance to implement malaria control measures and monitor their effectiveness. We use a previously developed amplicon panel (ANOSPP) that retrieves sequence data from multiple short nuclear loci for any species in the genus. Species assignment is based on comparison of samples to a reference index using k-mer distance. Here, we provide a protocol to generate version controlled updates of the reference index and present its latest release, NNv2, which contains 91 species, compared to 56 species represented in its predecessor NNv1. With the updated reference index, we are able to assign samples to species level that previously could not be assigned. We discuss what happens if a species is not represented in the reference index and how this can be addressed in a future update. To demonstrate the increased power of NNv2, we showcase the assignments of 1789 wild-caught mosquitoes from Madagascar and demonstrate that we can detect within species population structure from the amplicon sequencing data.