@article{fdi:010075737,
  title = {{O}ne-locus-several-primers : a strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies},
  author = {{C}orse, {E}. and {T}ougard, {C}. and {A}rchambaud-{S}uard, {G}. and {A}gn{\`e}se, {J}ean-{F}ran{\c{c}}ois and {M}andeng, {F}. {D}. {M}. and {B}ilong, {C}. {F}. {B}. and {D}uneau, {D}. and {Z}inger, {L}. and {C}happaz, {R}. and {X}u, {C}. {C}. {Y}. and {M}eglecz, {E}. and {D}ubut, {V}.},
  editor = {},
  language = {{ENG}},
  abstract = {{I}n diet metabarcoding analyses, insufficient taxonomic coverage of {PCR} primer sets generates false negatives that may dramatically distort biodiversity estimates. {I}n this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit {I} gene ({COI}) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. {O}ur results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [{MOTU}s] and variants). {W}e then formalized the one-locus-several-primer-sets ({OLSP}) strategy, that is, the use of several primer sets that target the same locus (here the first part of the {COI} gene) and the same group of taxa (here invertebrates). {T}he proximal aim of the {OLSP} strategy is to minimize false negatives by increasing total coverage through multiple primer sets. {W}e illustrate that the {OLSP} strategy is especially relevant from this perspective since distinct variants within the same {MOTU}s were not equally detected across all primer sets. {F}urthermore, the {OLSP} strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. {T}his facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey-predator interactions.},
  keywords = {cytochrome c oxidase subunit {I} gene ; diet analysis ; e{DNA} ; false negatives ; metabarcoding ; {PCR} primers},
  booktitle = {},
  journal = {{E}cology and {E}volution},
  volume = {9},
  numero = {8},
  pages = {4603--4620},
  ISSN = {2045-7758},
  year = {2019},
  DOI = {10.1002/ece3.5063},
  URL = {https://www.documentation.ird.fr/hor/fdi:010075737},
}