One‐locus‐several‐primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

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‐lo..., Villsen2023_ITV_sample_fastq_correspondence.csv
CSV file with tag combinations to identify the samples and technical replicates from each fastq file
Villsen2023_ITV _Metabarcoding_Filtered_Data.csv
CSV file reporting the metabarcoding data that past the filtering procedure. The data include ASVs and contigs, sequence data, and taxonomic assignment for Zingel asper’s feces.
Villsen2023_ITV_dietdata.csv
CSV file reporting the diet data used to estimate individual and population trophic traits of Zingel asper.Please note that columns of Villsen2023_ITV_dietdata.csv correspond to rows in Villsen2023_ITV _Metabarcoding_Filtered_Data.csv
Villsen2023_ITV_HabitatPreydata.csv
Macroinvertebrate and habitat datasets used for statistical analysis and modelling process in Villsen2023_ITV
README_Villsen2023_ITV_HabitatPreydata.txt
List of variables in Villsen2023_ITV_HabitatPreydata.csv
 
Villsen2022_sample_fastq_correspondence.csv
CSV file with tag combinations to identify the samples and technical ...,