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The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms.

Beck C, Knoop H, Axmann IM, Steuer R - BMC Genomics (2012)

Bottom Line: We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality.Our 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Theoretical Biology, Humboldt-University of Berlin, Invalidenstr, 43, D-10115 Berlin, Germany.

ABSTRACT

Background: Cyanobacteria 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.

Results: Here, 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.

Conclusions: Our 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.

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Distribution of CLOGs across 16 cyanobacterial genomes. A - A histogram of the number of assigned strains to each CLOG. We distinguish between core CLOGs (660 CLOGs, assigned to all 16 strains), shared CLOGs (6668 CLOGs, assigned to 2-15 strains), and unique CLOGs (13910 CLOGs, assigned to a unique strain). B - Number of CLOGs assigned to each strain, highlighting the contribution of core, shared, and unique CLOGs.
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Figure 2: Distribution of CLOGs across 16 cyanobacterial genomes. A - A histogram of the number of assigned strains to each CLOG. We distinguish between core CLOGs (660 CLOGs, assigned to all 16 strains), shared CLOGs (6668 CLOGs, assigned to 2-15 strains), and unique CLOGs (13910 CLOGs, assigned to a unique strain). B - Number of CLOGs assigned to each strain, highlighting the contribution of core, shared, and unique CLOGs.

Mentions: To obtain insight into the organization of the cyanobacterial genomic diversity, each CLOG is assigned to a cyanobacterial strain if one or more member of a CLOG is present in the respective genome. Figure 2A shows a histogram of the number of CLOGs as a function of the number of associated strains. We can distinguish between core genes (660 CLOGs), those that are assigned to all 16 strains, shared genes (6668 CLOGs), those that are found in more than one but not in all strains, and unique genes (13910 CLOGs) that have no likely ortholog in any other of the 15 genome sequences. Figure 2B shows the number of CLOGs assigned to each cyanbacterial species, highlighting the contribution of core, shared, and unique CLOGs. The data is provided as Additional File 2.


The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms.

Beck C, Knoop H, Axmann IM, Steuer R - BMC Genomics (2012)

Distribution of CLOGs across 16 cyanobacterial genomes. A - A histogram of the number of assigned strains to each CLOG. We distinguish between core CLOGs (660 CLOGs, assigned to all 16 strains), shared CLOGs (6668 CLOGs, assigned to 2-15 strains), and unique CLOGs (13910 CLOGs, assigned to a unique strain). B - Number of CLOGs assigned to each strain, highlighting the contribution of core, shared, and unique CLOGs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3369817&req=5

Figure 2: Distribution of CLOGs across 16 cyanobacterial genomes. A - A histogram of the number of assigned strains to each CLOG. We distinguish between core CLOGs (660 CLOGs, assigned to all 16 strains), shared CLOGs (6668 CLOGs, assigned to 2-15 strains), and unique CLOGs (13910 CLOGs, assigned to a unique strain). B - Number of CLOGs assigned to each strain, highlighting the contribution of core, shared, and unique CLOGs.
Mentions: To obtain insight into the organization of the cyanobacterial genomic diversity, each CLOG is assigned to a cyanobacterial strain if one or more member of a CLOG is present in the respective genome. Figure 2A shows a histogram of the number of CLOGs as a function of the number of associated strains. We can distinguish between core genes (660 CLOGs), those that are assigned to all 16 strains, shared genes (6668 CLOGs), those that are found in more than one but not in all strains, and unique genes (13910 CLOGs) that have no likely ortholog in any other of the 15 genome sequences. Figure 2B shows the number of CLOGs assigned to each cyanbacterial species, highlighting the contribution of core, shared, and unique CLOGs. The data is provided as Additional File 2.

Bottom Line: We describe genetic diversity found within cyanobacterial genomes, specifically with respect to metabolic functionality.Our 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Theoretical Biology, Humboldt-University of Berlin, Invalidenstr, 43, D-10115 Berlin, Germany.

ABSTRACT

Background: Cyanobacteria 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.

Results: Here, 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.

Conclusions: Our 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.

Show MeSH
Related in: MedlinePlus