We agree with the reviewer’s concern. In fact, this is exactly the reason why we chose Cyanobacteria for this analysis. We reformulated this part of the introduction, to make this statement more clear, which now reads: “We choose Cyanobacteria as an example of prokaryotes, not because they are representative for all prokaryotes, but because there is ample phenotypic, ecological, physiological ultrastructural, and biochemical evidence of the existence of independently evolving units in this group [20,21]. Thus, the expectation is that, if a barcoding gap exists in prokaryotes, this should be more easily seen in taxa where groups can be identified also with other methods, as in Cyanobacteria.”
I am not sure that cyanobacteria can be accepted as a typical example of all prokaryotes. On the contrary, they have very special position (phylogenetic, metabolic, function in nature, ultrastructural, they grow often in multicellular and differentiated thallus) and their diversity must be evaluated respecting these specificities. It is clear that the taxonomic classification must be different in different groups of organisms.