AUTHOR=Boddé Marilou , Makunin Alex , Teltscher Fiona , Akorli Jewelna , Andoh Nana Efua , Bei Amy , Chaumeau Victor , Desamours Ife , Ekpo Uwem F. , Govella Nicodem J. , Kayondo Jonathan , Kobylinski Kevin , Ngom Elhadji Malick , Niang El Hadji Amadou , Okumu Fredros , Omitola Olaitan O. , Ponlawat Alongkot , Rakotomanga Malala Nirina , Rasolonjatovoniaina Mialy Tatamo , Ayala Diego , Lawniczak Mara 

TITLE=Improved species assignments across the entire Anopheles genus using targeted sequencing

JOURNAL=Frontiers in Genetics

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1456644

DOI=10.3389/fgene.2024.1456644

ISSN=1664-8021

ABSTRACT=<p>Accurate species identification of the mosquitoes in the genus <italic>Anopheles</italic> 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 <italic>k</italic>-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.</p>