Nanopore /Illumina/IonTorrent DNA sequencing comparison
Individual sorting and identification of thousands of insects collected in mass trapping biosurveillance programs is a labor intensive and time-consuming process. Metabarcoding, which allows for the simultaneous identification of multiple individuals in a single mixed sample, has the potential to expedite this process. However, detecting all the species present in a bulk sample can be challenging. In this study, we quantified the effectiveness of metabarcoding at detecting all species in six different mock communities of xylophagous cerambycid beetles. We also assessed the effect of conservation trapping methods, sequencing technologies and primer choice on species recovery. No significant differences in the number of species detected were observed between MinION, Illumina, and IonTorrent sequencing technologies, although MinION detected a greater number of species. The capture method greatly influences sample preservation and detection. Indeed, individuals captured using monopropylene and water had both lower DNA concentration and species detection rates compared to individuals killed using just an insecticide without any collection medium.