Abstract
BackgroundCyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics. As the only known prokaryotes capable of oxygenic photosynthesis, cyanobacteria are considered to be a promising resource for renewable fuels and natural products. Our efforts to harness the sun's energy using cyanobacteria would greatly benefit from an increased understanding of the genomic diversity across multiple cyanobacterial strains. In this respect, the advent of novel sequencing techniques and the availability of several cyanobacterial genomes offers new opportunities for understanding microbial diversity and metabolic organization and evolution in diverse environments.ResultsHere, we report a whole genome comparison of multiple phototrophic cyanobacteria. We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality. Our results are based on pair-wise comparison of protein sequences and concomitant construction of clusters of likely ortholog genes. We differentiate between core, shared and unique genes and show that the majority of genes are associated with a single genome. In contrast, genes with metabolic function are strongly overrepresented within the core genome that is common to all considered strains. The analysis of metabolic diversity within core carbon metabolism reveals parts of the metabolic networks that are highly conserved, as well as highly fragmented pathways.ConclusionsOur results have direct implications for resource allocation and further sequencing projects. It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes. Furthermore, genome analysis of multiple phototrophic strains allows us to obtain a detailed picture of metabolic diversity that can serve as a starting point for biotechnological applications and automated metabolic reconstructions.
Highlights
Cyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics
The chosen strains are not restricted to a single genus but were selected to represent the known genomic and metabolic diversity found in the cyanobacterial phylum, including eight marine and eight freshwater strains
We have presented a whole genome analysis of multiple phototrophic cyanobacteria, with the aim to gain insight into the diversity of cyanobacterial metabolism from a genome perspective
Summary
Cyanobacteria are among the most abundant organisms on Earth and represent one of the oldest and most widespread clades known in modern phylogenetics. Our efforts to harness the sun’s energy using cyanobacteria would greatly benefit from an increased understanding of the genomic diversity across multiple cyanobacterial strains In this respect, the advent of novel sequencing techniques and the availability of several cyanobacterial genomes offers new opportunities for understanding microbial diversity and metabolic organization and evolution in diverse environments. Raymond et al [5] have previously compared five whole genome sequences from all groups of photosynthetic prokaryotes, with the aim to identify genes that play an essential role in phototrophy and to understand the advent and developement of photosynthesis Their results showed that the genomes of the studied organisms resemble mosaics of genes with very different evolutionary histories and that orthologs common to all five genomes showed a distinct lack of unanimous support for any single phylogenetic topology. Several ocean sampling expeditions investigated microbial diversity in marine environments [10,11], again confirming substantial oceanic microbial diversity and considerable heterogeneity of microorganisms at the genomic level, for Prochlorococcus, one of the most abundant genus of cyanobacteria
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