Improved species assignments across the entire Anopheles genus using targeted sequencing
Accurate species identification of the mosquitoes in the genus <i>Anopheles</i> 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 <i>k</i>-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.
Authors
- Fredros O. Okumu
- Nicodem James Govella (ORCID: https://orcid.org/0000-0001-5460-9629)
- Diégo Ayala (ORCID: https://orcid.org/0000-0003-4726-580X)
- Jonathan Kayondo (ORCID: https://orcid.org/0000-0003-0877-6877)
- Uwem Friday Ekpo (ORCID: https://orcid.org/0000-0002-0543-5463)
- Jewelna Akorli (ORCID: https://orcid.org/0000-0002-3972-0860)
- Nana Efua Andoh (ORCID: https://orcid.org/0000-0002-6678-3269)
- El Hadji Amadou Niang (ORCID: https://orcid.org/0000-0001-5611-1998)
- Amy K. Bei (ORCID: https://orcid.org/0000-0003-1159-760X)
- Victor Chaumeau (ORCID: https://orcid.org/0000-0003-0171-2176)
- Fiona Teltscher (ORCID: https://orcid.org/0000-0001-9987-6691)
- Malala Nirina Rakotomanga
- Olaitan Olamide Omitola (ORCID: https://orcid.org/0000-0003-3827-6320)
- Alex Makunin (ORCID: https://orcid.org/0000-0002-9555-5097)
- Alongkot Ponlawat (ORCID: https://orcid.org/0000-0001-8196-5514)
- Ife Desamours
- Mara Lawniczak (ORCID: https://orcid.org/0000-0002-3006-2080)
- Marilou Boddé (ORCID: https://orcid.org/0000-0003-2107-5100)
- Kevin C. Kobylinski (ORCID: https://orcid.org/0000-0002-4807-9681)
- Elhadji Malick Ngom
- Mialy Tatamo Rasolonjatovoniaina
Institutions
- Ifakara Health Institute (TZ)
- Centre National de la Recherche Scientifique (FR)
- Federal University of Agriculture, Abeokuta (NG)
- University of Cambridge (GB)
- Agropolis International (FR)
- Wellcome Sanger Institute (GB)
- Leibniz Association (DE)
- Yale University (US)
- University of Oxford (GB)
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (FR)
- Noguchi Memorial Institute for Medical Research (GH)
- Shoklo Malaria Research Unit (TH)
- Institute for Biodiversity (DE)
- Armed Forces Research Institute of Medical Science (TH)
- Mahidol Oxford Tropical Medicine Research Unit (TH)
- Institut Pasteur de Madagascar (MG)
- Institut Pasteur de Dakar (SN)
- Institut de Recherche pour le Développement (FR)
- Leibniz Institute for the Analysis of Biodiversity Change (DE)
- Uganda Virus Research Institute (UG)
- Cheikh Anta Diop University (SN)
Publication Details
- Journal
- Frontiers in Genetics
- Published
- 2024-09-19
- DOI
- https://doi.org/10.3389/fgene.2024.1456644
- Citations
- 4
- Primary Topic
- Mosquito-borne diseases and control
- Type
- article
- Field-Weighted Citation Impact
- 2.17
Funders
- Bill and Melinda Gates Foundation
- Wellcome Trust