Cyanobacteria are amongst the most important primary producers on the Earth. However, the evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macroorganisms, and an undersampling of sequenced genomes. Thus, we present a new genome of a Synechococcus-like cyanobacterium from a novel evolutionary lineage. Further, we analyse all existing 16S rRNA sequences and genomes of Synechococcus-like cyanobacteria. Chronograms showed extremely polyphyletic relationships in Synechococcus, which has not been observed in any other cyanobacteria. Moreover, most Synechococcus lineages bifurcated after the Great Oxidation Event, including the most abundant marine picoplankton lineage. Quantification of horizontal gene transfer among 70 cyanobacterial genomes revealed significant differences among studied genomes. Horizontal gene transfer levels were not correlated with ecology, genome size, or phenotype, but were correlated with the age of divergence. All findings were synthetized into a novel model of cyanobacterial evolution, characterized by serial convergence of the features, i.e. multicellularity and ecology.

Multiple sequence alignment for phylogenomic analysisProtein Multiple sequence alignment recovered from Bio-Hal for phylogenetic analysis in Phylip format. There are 70 taxa and more than 46000 positions.Biohal2.phyPhylogenetic tree based on protein super alignmentPhylogenetic tree based on protein super alignment constructed in RaxML 8.0. Abbrevations of OTUs are explained in ReadMe file.raxmlTreeDryad.treMultiple sequence alignment of 16S rRNAMultiple sequence alignment of 16S rRNA of diverse cyanobacteria with focus on Synechococcus.allsynech19.nex16S rRNA phylogenetic treeA phylogenetic tree constructed using MrBayes 3.2.216SalignDryad.nex