Publications des scientifiques de l'IRD

Corse E., Tougard C., Archambaud-Suard G., Agnèse Jean-François, Mandeng F. D. M., Bilong C. F. B., Duneau D., Zinger L., Chappaz R., Xu C. C. Y., Meglecz E., Dubut V. (2019). One-locus-several-primers : a strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies. Ecology and Evolution, 9 (8), p. 4603-4620. ISSN 2045-7758.

Titre du document
One-locus-several-primers : a strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies
Année de publication
2019
Type de document
Article référencé dans le Web of Science WOS:000466104200024
Auteurs
Corse E., Tougard C., Archambaud-Suard G., Agnèse Jean-François, Mandeng F. D. M., Bilong C. F. B., Duneau D., Zinger L., Chappaz R., Xu C. C. Y., Meglecz E., Dubut V.
Source
Ecology and Evolution, 2019, 9 (8), p. 4603-4620 ISSN 2045-7758
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In 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. Our 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 [MOTUs] and variants). We 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). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey-predator interactions.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Limnologie biologique / Océanographie biologique [034] ; Sciences du monde animal [080]
Localisation
Fonds IRD [F B010075737]
Identifiant IRD
fdi:010075737
Contact