Limits...
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

Show MeSH

Related in: MedlinePlus

Overview of 16 cyanophage genome annotations. Each drawn box represents a predicted open reading frame (ORF) with forward strand ORFs above and reverse strand ORFs below. ORFs are colour-coded as per the legend in the figure, while colour-coded lines on the genome represent experimentally determined structural proteins (see Experimental procedures). For spreadsheet version of these data, please see File S1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3037559&req=5

fig01: Overview of 16 cyanophage genome annotations. Each drawn box represents a predicted open reading frame (ORF) with forward strand ORFs above and reverse strand ORFs below. ORFs are colour-coded as per the legend in the figure, while colour-coded lines on the genome represent experimentally determined structural proteins (see Experimental procedures). For spreadsheet version of these data, please see File S1.

Mentions: All available annotation information for the 16 cyanophage genomes is provided in a detailed overview figure (Fig. 1). With two exceptions, cyanophage genome sizes ranged from 174 to 196 kb (summarized in Table 1, details provided in Table S1), as commonly observed previously for non-cyanophages (Miller et al., 2003a,b; Nolan et al., 2006; Petrov et al., 2006). The exceptional cyanophages were S-SSM7 (232 kb) and P-SSM2 (252 kb), which contained large lipopolysaccharide gene clusters (Fig. 1, discussed below) that accounted for about 72–85% of the expanded genome size. Cyanophage genome size was correlated with the number of predicted open reading frames (ORFs) (R2 = 0.743), and there was no apparent relationship between the genome size and the genus of the host on which it was isolated (Fig. S1).


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)

Overview of 16 cyanophage genome annotations. Each drawn box represents a predicted open reading frame (ORF) with forward strand ORFs above and reverse strand ORFs below. ORFs are colour-coded as per the legend in the figure, while colour-coded lines on the genome represent experimentally determined structural proteins (see Experimental procedures). For spreadsheet version of these data, please see File S1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig01: Overview of 16 cyanophage genome annotations. Each drawn box represents a predicted open reading frame (ORF) with forward strand ORFs above and reverse strand ORFs below. ORFs are colour-coded as per the legend in the figure, while colour-coded lines on the genome represent experimentally determined structural proteins (see Experimental procedures). For spreadsheet version of these data, please see File S1.
Mentions: All available annotation information for the 16 cyanophage genomes is provided in a detailed overview figure (Fig. 1). With two exceptions, cyanophage genome sizes ranged from 174 to 196 kb (summarized in Table 1, details provided in Table S1), as commonly observed previously for non-cyanophages (Miller et al., 2003a,b; Nolan et al., 2006; Petrov et al., 2006). The exceptional cyanophages were S-SSM7 (232 kb) and P-SSM2 (252 kb), which contained large lipopolysaccharide gene clusters (Fig. 1, discussed below) that accounted for about 72–85% of the expanded genome size. Cyanophage genome size was correlated with the number of predicted open reading frames (ORFs) (R2 = 0.743), and there was no apparent relationship between the genome size and the genus of the host on which it was isolated (Fig. S1).

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