We agree that this might be confusing to the reader. We have therefore clarified this choice and added this part to the first M&M section and the literature suggested has been cited: “Sequences termed Synechococcus on the other hand were analysed together with sequences of Prochlorococcus, since Synechococcus is known to be a polyphyletic group and if all sequences (including a minimum of five lineages [36–38]) are taken together, Prochlorococcus has to be included too.”
It is overall well-written and innovative work, but there are few things to consider in methods and results, which should be revised, and some formal flaws. When you refer to the Synechococcus, it is important to specify, which clade you have in mind. Honda et al. (1999) and Roberston et al. (2001) showed Synechococcus is polyphyletic genus composed of a least 5 lineages. There are more recent works showing even more clades. From an amount of sequences and relationship to Prochlorococcus, I can assume, it is a marine pelagial picoplanktic clade. However, it should be specified for unexperienced reader in the field of cyanobacteria. The other polyphyletic genera should be also specified—Phormidium, Leptolyngbya, Microcoleus and others. Moreover, although the sequences might have same name (i.e., Synechococcus), they belong to polyphyletic groups, thus they probably belong to different genera, which have not yet been described.