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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 scaffolds containing the g23 MCP gene. Schematic of the scaffolds containing g23, with each gene/ORF (rectangles) colored to match its origin type, compared with the cultured Cyano-T4 genomes in this region. Those g23s that do not represent the majority origin type on the scaffolds or genomes are marked with an “X.” Due to space considerations, some of the genes/ORFs of known origin have been condensed (e.g., “x3”), and some ORFans have been omitted. The phylogenetic tree inset shows the relationships among the Cyano-T4 gp23 proteins, with T4 as the outgroup and the scale bar indicating 0.1 substitutions per site.
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fig3: GOS scaffolds containing the g23 MCP gene. Schematic of the scaffolds containing g23, with each gene/ORF (rectangles) colored to match its origin type, compared with the cultured Cyano-T4 genomes in this region. Those g23s that do not represent the majority origin type on the scaffolds or genomes are marked with an “X.” Due to space considerations, some of the genes/ORFs of known origin have been condensed (e.g., “x3”), and some ORFans have been omitted. The phylogenetic tree inset shows the relationships among the Cyano-T4 gp23 proteins, with T4 as the outgroup and the scale bar indicating 0.1 substitutions per site.

Mentions: The straightforward answer to this question is yes—on a “coarse” scale (separating T4-like subgroups), the scaffold phage genes in the three marker regions (n = 535) were almost exclusively (99%) of Cyano-T4 origin. There was only one gene from a non–T4-like phage (myovirus BcepB1A) and a few cellular hits and ORFans. There was “fine-scale mosaicism” in the sense that the scaffolds, and the cultured Cyano-T4 genomes themselves, are mixtures of different “specific” Cyano-T4–type genes (e.g. Syn9-like genes may be next to P-SSM2-like genes, etc.). However, one phylogenetic isolate is generally predominant; for example, most of the GOS scaffolds were P-SSM2 like in the marker regions. The most “faithful” marker gene was g23—only four, often small, scaffolds (of 20 total) had MCPs whose phylogenetic origins did not precisely match with the majority of the scaffold's genes (fig. 3).


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 scaffolds containing the g23 MCP gene. Schematic of the scaffolds containing g23, with each gene/ORF (rectangles) colored to match its origin type, compared with the cultured Cyano-T4 genomes in this region. Those g23s that do not represent the majority origin type on the scaffolds or genomes are marked with an “X.” Due to space considerations, some of the genes/ORFs of known origin have been condensed (e.g., “x3”), and some ORFans have been omitted. The phylogenetic tree inset shows the relationships among the Cyano-T4 gp23 proteins, with T4 as the outgroup and the scale bar indicating 0.1 substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: GOS scaffolds containing the g23 MCP gene. Schematic of the scaffolds containing g23, with each gene/ORF (rectangles) colored to match its origin type, compared with the cultured Cyano-T4 genomes in this region. Those g23s that do not represent the majority origin type on the scaffolds or genomes are marked with an “X.” Due to space considerations, some of the genes/ORFs of known origin have been condensed (e.g., “x3”), and some ORFans have been omitted. The phylogenetic tree inset shows the relationships among the Cyano-T4 gp23 proteins, with T4 as the outgroup and the scale bar indicating 0.1 substitutions per site.
Mentions: The straightforward answer to this question is yes—on a “coarse” scale (separating T4-like subgroups), the scaffold phage genes in the three marker regions (n = 535) were almost exclusively (99%) of Cyano-T4 origin. There was only one gene from a non–T4-like phage (myovirus BcepB1A) and a few cellular hits and ORFans. There was “fine-scale mosaicism” in the sense that the scaffolds, and the cultured Cyano-T4 genomes themselves, are mixtures of different “specific” Cyano-T4–type genes (e.g. Syn9-like genes may be next to P-SSM2-like genes, etc.). However, one phylogenetic isolate is generally predominant; for example, most of the GOS scaffolds were P-SSM2 like in the marker regions. The most “faithful” marker gene was g23—only four, often small, scaffolds (of 20 total) had MCPs whose phylogenetic origins did not precisely match with the majority of the scaffold's genes (fig. 3).

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