Metabarcoding
I thought this paper was very enlightening. I think this paper highlights why it’s challenging to make a universal primer set. I wonder why the COI primer set the authors created performed poorly compared with the MiFish 12s. It seems like 12s is becoming the industry standard when metabarcoding fish. I think different gene regions are better for detecting specific taxa. COI isn’t great for fish and macroalgae. COI is suitable for other invertebrates. 28s is best for distinguishing red macroalgae. Ideally, we would build up all of these reference databases. COI has been the best for references because of the Barcode of Life initiative. However, just because it has more references doesn’t mean it is best to use for metabarcoding. I would prefer more unknown OTUs/ASVs and have an optimized primer set than a poor primer set that couldn’t distinguish species or detect a broad range of taxa. In this first situation, we could always build up those references and eventually assign taxa. However, if you have no more DNA left and sequence with a lousy primer set, it seems you’d be SOL.