RT Journal Article
SR Electronic
T1 Modules of co-occurrence in the cyanobacterial pan-genome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 137398
DO 10.1101/137398
A1 Christian Beck
A1 Henning Knoop
A1 Ralf Steuer
YR 2017
UL http://biorxiv.org/content/early/2017/05/12/137398.abstract
AB 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 CLOGs is indicative of functional relationships between the respective genes. Going beyond the analysis of pair-wise co-occurrences, we introduce a novel network approach to identify modules of co-occurring ortholog genes. 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.