Internal transcribed spacer primer evaluation for vascular plant metabarcoding

The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations In PCR based metabarcoding of plants, aside from picking a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities, and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavorable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimization, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that a continuous quality assurance is indispensable for reliable metabarcoding results.