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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

The core and pan-genomes of the (A) cyanophage and (B) non-cyanophage groups, where the core and pan-genomes are represented by square and triangles respectively. The core and pan-genomes were analysed for k genomes from cyanophages (n = 16) or non-cyanophages (n = 10). Each possible variation is shown as a grey point, and the line is drawn through the average. The core genome is defined as genes that are present in the selected k genomes. The pan-genome is the total unique genes found in k genomes. All variations of n choose k: n!/k!(n − k)!.
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fig03: The core and pan-genomes of the (A) cyanophage and (B) non-cyanophage groups, where the core and pan-genomes are represented by square and triangles respectively. The core and pan-genomes were analysed for k genomes from cyanophages (n = 16) or non-cyanophages (n = 10). Each possible variation is shown as a grey point, and the line is drawn through the average. The core genome is defined as genes that are present in the selected k genomes. The pan-genome is the total unique genes found in k genomes. All variations of n choose k: n!/k!(n − k)!.

Mentions: To explore the features of the core and pan-genomes of the cyanophage and non-cyanophage subsets given the number of genomes sequenced, we identified the shared and unshared gene sets of all possible combinations of choosing k genomes (k = 1 to n) from n sequenced genomes (Fig. 3). The core genes shared within the two groups (discussed in detail below) levelled off quickly as new genomes were added to the analysis, suggesting that this small sample size of diverse T4-like phages is adequate for determining the core. As expected, the total number of unique genes identified (the pan-genome) steadily increased with the number of available genomes in both cases. The size of the pan-genome reached 1388 and 1445 genes for the cyanophages and non-cyanophages respectively (Fig. 3A and B). The rate of increase of both pan-genomes as more genomes are added to the analysis is far from saturated, indicating the existence of a much larger and diverse gene pool than has been captured by the 26 sequenced genomes. Interestingly, however, the cyanophage pan-genome showed a slower rate of increase (Fig. 3A) than that of the non-cyanophages (Fig. 3B).


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)

The core and pan-genomes of the (A) cyanophage and (B) non-cyanophage groups, where the core and pan-genomes are represented by square and triangles respectively. The core and pan-genomes were analysed for k genomes from cyanophages (n = 16) or non-cyanophages (n = 10). Each possible variation is shown as a grey point, and the line is drawn through the average. The core genome is defined as genes that are present in the selected k genomes. The pan-genome is the total unique genes found in k genomes. All variations of n choose k: n!/k!(n − k)!.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig03: The core and pan-genomes of the (A) cyanophage and (B) non-cyanophage groups, where the core and pan-genomes are represented by square and triangles respectively. The core and pan-genomes were analysed for k genomes from cyanophages (n = 16) or non-cyanophages (n = 10). Each possible variation is shown as a grey point, and the line is drawn through the average. The core genome is defined as genes that are present in the selected k genomes. The pan-genome is the total unique genes found in k genomes. All variations of n choose k: n!/k!(n − k)!.
Mentions: To explore the features of the core and pan-genomes of the cyanophage and non-cyanophage subsets given the number of genomes sequenced, we identified the shared and unshared gene sets of all possible combinations of choosing k genomes (k = 1 to n) from n sequenced genomes (Fig. 3). The core genes shared within the two groups (discussed in detail below) levelled off quickly as new genomes were added to the analysis, suggesting that this small sample size of diverse T4-like phages is adequate for determining the core. As expected, the total number of unique genes identified (the pan-genome) steadily increased with the number of available genomes in both cases. The size of the pan-genome reached 1388 and 1445 genes for the cyanophages and non-cyanophages respectively (Fig. 3A and B). The rate of increase of both pan-genomes as more genomes are added to the analysis is far from saturated, indicating the existence of a much larger and diverse gene pool than has been captured by the 26 sequenced genomes. Interestingly, however, the cyanophage pan-genome showed a slower rate of increase (Fig. 3A) than that of the non-cyanophages (Fig. 3B).

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