Modules Of Co-Occurrence In The Cyanobacterial Pan-Genome

The increasing availability of fully sequenced cyanobacterial genomes opens unprecedented opportunities to investigate the manifold adaptations and functional relationships that determine the genetic content of individual bacterial species. Here, we use comparative genome analysis to investigate the cyanobacterial pan-genome, based on 77 strains whose complete genome sequence is available. Our focus is the co-occurrence of likely ortholog genes, denoted as CLOGs. We conjecture that co-occurrence of CLOGs is indicative of functional relationships between the respective genes. Going beyond the analysis of pair-wise co-occurrences, we introduce a network approach to identify modules of co-occurring CLOGs. Our results demonstrate that these modules exhibit a high degree of functional coherence and reveal known as well as previously unknown functional relationships. We argue that the high functional coherence observed for the extracted modules is a consequence of the similar-yet-diverse nature of the cyanobacterial phylum. We provide a simple toolbox that facilitates further analysis of our results with respect to specific cyanobacterial genes of interest.