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Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW - Environ. Microbiol. (2010)

Bottom Line: Patterns among non-core genes that may drive niche diversification revealed that phosphorus-related gene content reflects source waters rather than host strain used for isolation, and that carbon metabolism genes appear associated with putative mobile elements.However, no clear diagnostic genes emerged to distinguish these phage groups, suggesting blurred boundaries possibly due to cross-infection.Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts Institute of Technology, Cambridge, MA, USA. mbsulli@email.arizona.edu

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Related in: MedlinePlus

T4-like gene set relatedness representations.A. Venn diagram illustrating the hierarchical core gene sets among 26 T4-like genomes.B. T4-like phage presence/absence gene cluster network. T4 Gene Clusters (T4-GCs) were used to construct a network of phage genomes and gene clusters found in one or more of the 26 genomes. Genomes are represented as diamonds, with cyanophage genomes coloured blue and non-cyanophage coloured red. Non-core T4-GCs are represented as a light purple circle, core T4-GCs shared by all genomes are coloured dark purple. If a T4-GC is present in a phage genome, an edge (green line) is drawn between that genome and the associated T4-GC. Genomes sharing many T4-GCs are in close spatial proximity to each other in the network. A multifasta file with all ORFs examined in this study is provided to link specific ORFs, T4-GC assignments and functional annotation (File S2).
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fig02: T4-like gene set relatedness representations.A. Venn diagram illustrating the hierarchical core gene sets among 26 T4-like genomes.B. T4-like phage presence/absence gene cluster network. T4 Gene Clusters (T4-GCs) were used to construct a network of phage genomes and gene clusters found in one or more of the 26 genomes. Genomes are represented as diamonds, with cyanophage genomes coloured blue and non-cyanophage coloured red. Non-core T4-GCs are represented as a light purple circle, core T4-GCs shared by all genomes are coloured dark purple. If a T4-GC is present in a phage genome, an edge (green line) is drawn between that genome and the associated T4-GC. Genomes sharing many T4-GCs are in close spatial proximity to each other in the network. A multifasta file with all ORFs examined in this study is provided to link specific ORFs, T4-GC assignments and functional annotation (File S2).

Mentions: In preparation for analyses of gene content and order in the different genomes, we clustered orthologous genes into T4 Gene Clusters (‘T4-GCs’; see Experimental procedures), and used these to define core gene sets common to hierarchical groupings of the genomes (Fig. 2A, see discussion below). A total of 6798 predicted genes in the 26 genomes clustered into 892 T4-GCs, with 1873 genes remaining as singletons.


Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW - Environ. Microbiol. (2010)

T4-like gene set relatedness representations.A. Venn diagram illustrating the hierarchical core gene sets among 26 T4-like genomes.B. T4-like phage presence/absence gene cluster network. T4 Gene Clusters (T4-GCs) were used to construct a network of phage genomes and gene clusters found in one or more of the 26 genomes. Genomes are represented as diamonds, with cyanophage genomes coloured blue and non-cyanophage coloured red. Non-core T4-GCs are represented as a light purple circle, core T4-GCs shared by all genomes are coloured dark purple. If a T4-GC is present in a phage genome, an edge (green line) is drawn between that genome and the associated T4-GC. Genomes sharing many T4-GCs are in close spatial proximity to each other in the network. A multifasta file with all ORFs examined in this study is provided to link specific ORFs, T4-GC assignments and functional annotation (File S2).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037559&req=5

fig02: T4-like gene set relatedness representations.A. Venn diagram illustrating the hierarchical core gene sets among 26 T4-like genomes.B. T4-like phage presence/absence gene cluster network. T4 Gene Clusters (T4-GCs) were used to construct a network of phage genomes and gene clusters found in one or more of the 26 genomes. Genomes are represented as diamonds, with cyanophage genomes coloured blue and non-cyanophage coloured red. Non-core T4-GCs are represented as a light purple circle, core T4-GCs shared by all genomes are coloured dark purple. If a T4-GC is present in a phage genome, an edge (green line) is drawn between that genome and the associated T4-GC. Genomes sharing many T4-GCs are in close spatial proximity to each other in the network. A multifasta file with all ORFs examined in this study is provided to link specific ORFs, T4-GC assignments and functional annotation (File S2).
Mentions: In preparation for analyses of gene content and order in the different genomes, we clustered orthologous genes into T4 Gene Clusters (‘T4-GCs’; see Experimental procedures), and used these to define core gene sets common to hierarchical groupings of the genomes (Fig. 2A, see discussion below). A total of 6798 predicted genes in the 26 genomes clustered into 892 T4-GCs, with 1873 genes remaining as singletons.

Bottom Line: Patterns among non-core genes that may drive niche diversification revealed that phosphorus-related gene content reflects source waters rather than host strain used for isolation, and that carbon metabolism genes appear associated with putative mobile elements.However, no clear diagnostic genes emerged to distinguish these phage groups, suggesting blurred boundaries possibly due to cross-infection.Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts Institute of Technology, Cambridge, MA, USA. mbsulli@email.arizona.edu

Show MeSH
Related in: MedlinePlus