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A combination of phylogenomic and signature sequence-based (or phenetic) approaches was used to understand the evolutionary relationships among cyanobacteria. Phylogenetic trees were constructed for 34 cyanobacteria whose genomes have been sequenced, based on concatenated sequences for 45 conserved proteins and also the 16S rRNA gene. In parallel, sequence alignments of various proteins were examined to identify conserved indels (i.e. molecular signatures or synapomorphies) that are specific for either all cyanobacteria or their various clades in the phylogenetic trees. Of the &gt;40 molecular signatures described in this work, 15 are specific for all cyanobacteria. The other cyanobacterial clades that can now be identified and circumscribed in molecular terms by using these signatures include a deep-branching clade (clade A, corresponding to the subclass Gloeobacterophycidae), consisting of Gloeobacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B'a) (15 aa insert in EF-G); a clade comprising all other cyanobacteria except those from clade A [18 aa insert in DNA polymerase I (Pol I), 2 aa insert in the DnaX protein, 4 aa insert in TrpRS and 4-5 aa insert in tryptophan synthase beta subunit]; a clade (clade C, corresponding to the subclass Synechococcophycidae) of various marine unicellular Synechococcus and Prochlorococcus cyanobacteria (12 aa insert in Pol I, 3 aa insert in RpoB, 2 aa insert in KgsA, 6 aa insert in TyrRS, 2 aa insert in tRNA-mG1 transferase and 1 aa deletion in the RpoC protein); a clade of the low-B/A ecotype Prochlorococcus strains (5 aa deletion in LeuRS and 1 aa insert in the Ffh protein); a clade consisting of the Nostocales species/strains (subclass Nostocophycidae; 4 aa insert in the PetA protein and 5 aa insert in the ribosomal protein S3); a clade of the order Chroococcales (1 aa insert in RecA); a clade comprising the orders Nostocales, Oscillatoriales and Chroococcales [19 aa insert in DnaE, 13 aa insert in GDP-mannose pyrophosphorylase and 22-27 aa insert in NADP(H)-quinone oxidoreductase subunit D]. Two additional conserved indels in the translation-initiation factor IF-2 and riboflavin synthase alpha subunit suggest an intermediate placement of the Oscillatoriales in between the orders Nostocales and Chroococcales. The unique presence of these molecular signatures in all available sequences from the indicated groups of cyanobacteria, but not in any other cyanobacteria (or bacteria), indicates that these synapomorphies provide novel and potentially useful means for circumscription of several important taxonomic clades of cyanobacteria in more definitive terms. The species-distribution patterns of these synapomorphies also indicate that the plant/plastid homologues are not derived from the clade A or C cyanobacteria.

Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades