In this study, we characterised for the first time through DNA metabarcoding the omnivorous diet of the African wolf.
Metabarcoding raw data (c. 3.4 Gb; paird-read) were generated from 29 faecal samples of African wolf (Canis lupaster) collected in spring / summer 2016 in the province of Tlemcen, northwestern Algeria.
Three genes were amplified and co-sequenced to study the omnivorous diet of the species:
- 12S for vertebrates (Riaz et al. 2011; https://doi.org/10.1093/nar/gkr732),
- COI for arthropods (Zeale et al. 2011; https://doi.org/10.1111/j.1755-0998.2010.02920.x),
- trnl for plants (Taberlet et al. 2007; https://doi.org/10.1093/nar/gkl938).
DNA extraction was carried out from a subsample of c. 200 mg of each faeces using the QIAamp DNA Stool kit (Qiagen, Les Ulis, France) within the “Degraded DNA” platform of the Institut des Sciences de l'Evolution de Montpellier (ISEM).
In order to capture the broad dietary spectrum of the African wolf, three genetic markers were used to detect vertebrates (mitochondrial 12S ribosomal RNA—12S), arthropods (mitochondrial Cytochrome Oxidase subunit I—COI) and plants (chloroplastic trnl intron—trnl).
The amplicon libraries were built following a two-step amplification procedure adapted from the Illumina 16S Metagenomic Sequencing Library Preparation Guide (ref.15044223 rev. B).
After purification with magnetic beads (ratio: 1.5 X), PCR products were quantified with QuantiFluor® dsDNA System, and the final equimolar pool was sequenced on a MiSeq Illumina sequencer using the Reagent kit v2 (300 cycles).
