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Gene network visualization and quantitative synteny analysis of more than 300 marine T4-like phage scaffolds from the GOS metagenome.

Comeau AM, Arbiol C, Krisch HM - Mol. Biol. Evol. (2010)

Bottom Line: This assembly permits the examination of synteny (organization) of the genes on the scaffolds and their comparison with the genome sequences from cultured Cyano-T4s.We employ comparative genomics and a novel usage of network visualization software to show that the scaffold phylogenies are similar to those of the traditional marker genes they contain.Importantly, these uncultured metagenomic scaffolds quite closely match the organization of the "core genome" of the known Cyano-T4s.

View Article: PubMed Central - PubMed

Affiliation: Centre National de la Recherche Scientifique, UMR5100, Toulouse, France.

ABSTRACT
Bacteriophages (phages) are the most abundant biological entities in the biosphere and are the dominant "organisms" in marine environments, exerting an enormous influence on marine microbial populations. Metagenomic projects, such as the Global Ocean Sampling expedition (GOS), have demonstrated the predominance of tailed phages (Caudovirales), particularly T4 superfamily cyanophages (Cyano-T4s), in the marine milieu. Whereas previous metagenomic analyses were limited to gene content information, here we present a comparative analysis of over 300 phage scaffolds assembled from the viral fraction of the GOS data. This assembly permits the examination of synteny (organization) of the genes on the scaffolds and their comparison with the genome sequences from cultured Cyano-T4s. We employ comparative genomics and a novel usage of network visualization software to show that the scaffold phylogenies are similar to those of the traditional marker genes they contain. Importantly, these uncultured metagenomic scaffolds quite closely match the organization of the "core genome" of the known Cyano-T4s. This indicates that the current view of genome architecture in the Cyano-T4s is not seriously biased by being based on a small number of cultured phages, and we can be confident that they accurately reflect the diverse population of such viruses in marine surface waters.

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Related in: MedlinePlus

GOS myovirus scaffold content. Taxonomic distribution of the phage (A) and eubacterial hits (B).
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fig2: GOS myovirus scaffold content. Taxonomic distribution of the phage (A) and eubacterial hits (B).

Mentions: BLAST analysis of the gene content of the myovirus scaffolds confirmed their T4-like character as the overwhelming proportion of hits were to phage genes of the T4 superfamily (1 581 of 1 779 total; 89%), with other phage types accounting for merely 12 hits (table 1). The only other significant source of genes/ORFs was the Eubacteria domain, corresponding to only ∼10% of the hits. For the phage hits, Prochlorococcus phage P-SSM2 genes were the most frequently represented in the scaffolds, accounting for nearly half of the hits (fig. 2A). These were followed by genes from the three other sequenced Cyano-T4s in nearly equal proportions—Prochlorococcus phage P-SSM4 and Synechococcus phages S-PM2 and Syn9. The four cyanophages represented ∼97% of the best phage hits, which, in combination with our previous analysis of the major capsid protein (MCP) (Comeau and Krisch 2008), confirms the overwhelming abundance of cyanophage from the T4 superfamily in the marine environment. There were 167 eubacterial hits within the phage scaffolds (fig. 2B), distributed largely among the Proteobacteria (half in the alpha class) and the cyanobacteria (mostly Prochlorococcus and Synechococcus). The major classes of identifiable eubacterial gene/ORF functions were permeases/transport channels, proteins involved in various iron and phosphate functions, carbohydrate metabolism and DNA-modifying (nucleases, methylases) enzymes, and bacterial-encoded proteins of possible phage origin (supplementary table S1, Supplementary Material online).


Gene network visualization and quantitative synteny analysis of more than 300 marine T4-like phage scaffolds from the GOS metagenome.

Comeau AM, Arbiol C, Krisch HM - Mol. Biol. Evol. (2010)

GOS myovirus scaffold content. Taxonomic distribution of the phage (A) and eubacterial hits (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2908710&req=5

fig2: GOS myovirus scaffold content. Taxonomic distribution of the phage (A) and eubacterial hits (B).
Mentions: BLAST analysis of the gene content of the myovirus scaffolds confirmed their T4-like character as the overwhelming proportion of hits were to phage genes of the T4 superfamily (1 581 of 1 779 total; 89%), with other phage types accounting for merely 12 hits (table 1). The only other significant source of genes/ORFs was the Eubacteria domain, corresponding to only ∼10% of the hits. For the phage hits, Prochlorococcus phage P-SSM2 genes were the most frequently represented in the scaffolds, accounting for nearly half of the hits (fig. 2A). These were followed by genes from the three other sequenced Cyano-T4s in nearly equal proportions—Prochlorococcus phage P-SSM4 and Synechococcus phages S-PM2 and Syn9. The four cyanophages represented ∼97% of the best phage hits, which, in combination with our previous analysis of the major capsid protein (MCP) (Comeau and Krisch 2008), confirms the overwhelming abundance of cyanophage from the T4 superfamily in the marine environment. There were 167 eubacterial hits within the phage scaffolds (fig. 2B), distributed largely among the Proteobacteria (half in the alpha class) and the cyanobacteria (mostly Prochlorococcus and Synechococcus). The major classes of identifiable eubacterial gene/ORF functions were permeases/transport channels, proteins involved in various iron and phosphate functions, carbohydrate metabolism and DNA-modifying (nucleases, methylases) enzymes, and bacterial-encoded proteins of possible phage origin (supplementary table S1, Supplementary Material online).

Bottom Line: This assembly permits the examination of synteny (organization) of the genes on the scaffolds and their comparison with the genome sequences from cultured Cyano-T4s.We employ comparative genomics and a novel usage of network visualization software to show that the scaffold phylogenies are similar to those of the traditional marker genes they contain.Importantly, these uncultured metagenomic scaffolds quite closely match the organization of the "core genome" of the known Cyano-T4s.

View Article: PubMed Central - PubMed

Affiliation: Centre National de la Recherche Scientifique, UMR5100, Toulouse, France.

ABSTRACT
Bacteriophages (phages) are the most abundant biological entities in the biosphere and are the dominant "organisms" in marine environments, exerting an enormous influence on marine microbial populations. Metagenomic projects, such as the Global Ocean Sampling expedition (GOS), have demonstrated the predominance of tailed phages (Caudovirales), particularly T4 superfamily cyanophages (Cyano-T4s), in the marine milieu. Whereas previous metagenomic analyses were limited to gene content information, here we present a comparative analysis of over 300 phage scaffolds assembled from the viral fraction of the GOS data. This assembly permits the examination of synteny (organization) of the genes on the scaffolds and their comparison with the genome sequences from cultured Cyano-T4s. We employ comparative genomics and a novel usage of network visualization software to show that the scaffold phylogenies are similar to those of the traditional marker genes they contain. Importantly, these uncultured metagenomic scaffolds quite closely match the organization of the "core genome" of the known Cyano-T4s. This indicates that the current view of genome architecture in the Cyano-T4s is not seriously biased by being based on a small number of cultured phages, and we can be confident that they accurately reflect the diverse population of such viruses in marine surface waters.

Show MeSH
Related in: MedlinePlus