@article{fdi:010091924,
  title = {{I}mproved species assignments across the entire {A}nopheles genus using targeted sequencing},
  author = {{B}odd{\'e}, {M}. and {M}akunin, {A}. and {T}eltscher, {F}. and {A}korli, {J}. and {A}ndoh, {N}. {E}. and {B}ei, {A}. and {C}haumeau, {V}. and {D}esamours, {I}. and {E}kpo, {U}. {F}. and {G}ovella, {N}. {J}. and {K}ayondo, {J}. and {K}obylinski, {K}. and {N}gom, {E}. {M}. and {N}iang, {E}. {A}. and {O}kumu, {F}. and {O}mitola, {O}. {O}. and {P}onlawat, {A}. and {R}akotomanga, {M}. {N}. and {R}asolonjatovoniaina, {M}. {T}. and {A}yala, {D}iego and {L}awniczak, {M}.},
  editor = {},
  language = {{ENG}},
  abstract = {{A}ccurate species identification of the mosquitoes in the genus {A}nopheles is of crucial importance to implement malaria control measures and monitor their effectiveness. {W}e use a previously developed amplicon panel ({ANOSPP}) that retrieves sequence data from multiple short nuclear loci for any species in the genus. {S}pecies assignment is based on comparison of samples to a reference index using k-mer distance. {H}ere, we provide a protocol to generate version controlled updates of the reference index and present its latest release, {NN}v2, which contains 91 species, compared to 56 species represented in its predecessor {NN}v1. {W}ith the updated reference index, we are able to assign samples to species level that previously could not be assigned. {W}e discuss what happens if a species is not represented in the reference index and how this can be addressed in a future update. {T}o demonstrate the increased power of {NN}v2, we showcase the assignments of 1789 wild-caught mosquitoes from {M}adagascar and demonstrate that we can detect within species population structure from the amplicon sequencing data.},
  keywords = {vector monitoring ; malaria vector ; species assignment ; {A}nopheles ; amplicon panel ; {GHANA} ; {GABON} ; {MADAGASCAR} ; {TANZANIE} ; {SENEGAL}},
  booktitle = {},
  journal = {{F}rontiers in {G}enetics},
  volume = {15},
  numero = {},
  pages = {1456644 [15 p.]},
  year = {2024},
  DOI = {10.3389/fgene.2024.1456644},
  URL = {https://www.documentation.ird.fr/hor/fdi:010091924},
}