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

Whole-genome pairwise comparisons across the bounds of the cyano T4 phage genome diversity are examined here. In all three panels, two genomes are compared where lines between the genomes connect homologues, coloured ORFs indicate genes that are unique to one genome or the other, and the per cent identity of each ORF is plotted in the lower half of each panel. Pairwise genome comparisons are presented for (A) two co-isolated cyanophages, P-HM1 and P-HM2, as well as (B) the three closest non-co-isolated phages, P-RSM4, S-SSM5 and S-SM1, and (C) the three most distant non-co-isolated phages, P-SSM2, S-PM2, Syn9, among the 16 sequenced cyanophage genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig04: Whole-genome pairwise comparisons across the bounds of the cyano T4 phage genome diversity are examined here. In all three panels, two genomes are compared where lines between the genomes connect homologues, coloured ORFs indicate genes that are unique to one genome or the other, and the per cent identity of each ORF is plotted in the lower half of each panel. Pairwise genome comparisons are presented for (A) two co-isolated cyanophages, P-HM1 and P-HM2, as well as (B) the three closest non-co-isolated phages, P-RSM4, S-SSM5 and S-SM1, and (C) the three most distant non-co-isolated phages, P-SSM2, S-PM2, Syn9, among the 16 sequenced cyanophage genomes.

Mentions: To explore genomic diversity among spatially coexisting phages capable of infecting the same host, we included in this sequencing project two phages isolated from the same water sample on the same host strain (Fig. 4A). These two cyanophages, P-HM1 and P-HM2, are highly syntenic and share 200 of 241 and 242 genes, respectively, whose protein sequences are on average 83% identical (Fig. 4A). In contrast, pairwise genome comparisons showed that among the non-co-isolated cyanophages, the genomes share as much as 77–80% of their genes with average identity 72–75% (Fig. 4B) or at the least 22–33% of their genes, with only 48–49% average identity (Fig. 4C).


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)

Whole-genome pairwise comparisons across the bounds of the cyano T4 phage genome diversity are examined here. In all three panels, two genomes are compared where lines between the genomes connect homologues, coloured ORFs indicate genes that are unique to one genome or the other, and the per cent identity of each ORF is plotted in the lower half of each panel. Pairwise genome comparisons are presented for (A) two co-isolated cyanophages, P-HM1 and P-HM2, as well as (B) the three closest non-co-isolated phages, P-RSM4, S-SSM5 and S-SM1, and (C) the three most distant non-co-isolated phages, P-SSM2, S-PM2, Syn9, among the 16 sequenced cyanophage genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig04: Whole-genome pairwise comparisons across the bounds of the cyano T4 phage genome diversity are examined here. In all three panels, two genomes are compared where lines between the genomes connect homologues, coloured ORFs indicate genes that are unique to one genome or the other, and the per cent identity of each ORF is plotted in the lower half of each panel. Pairwise genome comparisons are presented for (A) two co-isolated cyanophages, P-HM1 and P-HM2, as well as (B) the three closest non-co-isolated phages, P-RSM4, S-SSM5 and S-SM1, and (C) the three most distant non-co-isolated phages, P-SSM2, S-PM2, Syn9, among the 16 sequenced cyanophage genomes.
Mentions: To explore genomic diversity among spatially coexisting phages capable of infecting the same host, we included in this sequencing project two phages isolated from the same water sample on the same host strain (Fig. 4A). These two cyanophages, P-HM1 and P-HM2, are highly syntenic and share 200 of 241 and 242 genes, respectively, whose protein sequences are on average 83% identical (Fig. 4A). In contrast, pairwise genome comparisons showed that among the non-co-isolated cyanophages, the genomes share as much as 77–80% of their genes with average identity 72–75% (Fig. 4B) or at the least 22–33% of their genes, with only 48–49% average identity (Fig. 4C).

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