Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.
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.
Affiliation: Massachusetts Institute of Technology, Cambridge, MA, USA. firstname.lastname@example.orgShow MeSH
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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).
Affiliation: Massachusetts Institute of Technology, Cambridge, MA, USA. email@example.com