Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage

Abstract

Viruses have been suggested to be the largest source of genetic diversity on Earth. Genome sequencing and metagenomic surveys reveal that novel genes with unknown functions are abundant in viral genomes. Yet few observations exist for the processes and frequency by which these genes are gained and lost. The surface waters of marine environments are dominated by marine picocyanobacteria and their co-existing viruses (cyanophages). Recent genome sequencing of cyanophages has revealed a vast array of genes that have been acquired from their cyanobacterial hosts. Here, we re-sequenced the cyanophage S-PM2 genome after 10 years of near continuous passage through its marine Synechococcus host. During this time a spontaneous mutant (S-PM2d) lacking 13% of the S-PM2 ORFs became dominant in the cyanophage population. These ORFs are found at one loci and are not homologous to any proteins in any other sequenced organism (ORFans). We demonstrate a fitness cost to S-PM2WT associated with possession of these ORFs under standard laboratory growth. Metagenomic surveys reveal these ORFs are present in various aquatic environments, are likely of cyanophage origin and appear to be enriched in environments from the extremes of salinity (freshwater and hypersaline). We posit that these ORFs contribute to the flexible gene content of cyanophages and offer a distinct fitness advantage in freshwater and hypersaline environments.

Viruses Inhibit CO 2 Fixation in the Most Abundant Phototrophs on Earth

“…WH7803 was grown in ASW medium in continuous light (25)(26)(27)(28)(29)(30) mmol photons m À2 s À1 ) at 23 C to an OD 750 nm between 0.35 and 0.40. Cell concentrations were measured using flow cytometry (FACScan, Becton Dickinson) and diluted to a concentration of 1 3 10 8 cells/ml with fresh ASW medium [44].…”

Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution

“…Previously, it was suggested that these unique genes probably encode specific enzymes or proteins for the cyanophage life cycle [43,44]. However, comparative genomic analyses have demonstrated that the majority of them show high similarity with cellular homologues of host cyanobacterial origin at the DNA sequence level [45,46]. There are many studies showing evidence of cyanophage acquisition of host genes encoding proteins or enzymes in key metabolic processes [47,48,49].…”

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

“…This phage is probably a result of a low-level contaminant in the stock of S-PM2d that was only detected due to the very high depth of initial sequencing coverage (> 2,000×). This contaminant has not been detected previously in S-PM2d which was recently purified by three rounds of plaque assay and sequenced to a high depth of coverage ( Puxty et al, 2015 ).…”

“…The dearth of reference phage genomes infecting cells of a particular genera is highlighted by the estimation of 5,476 viral populations in the upper oceans, of which only 39 could be affiliated to cultured viruses ( Brum et al, 2015 ). Re-sequencing of cultured phage genomes also provides insight into their genome evolution ( Puxty et al, 2015 ). Altogether, it is clear that there exists a developing need for a high-throughput approach to the sequencing and re-sequencing of cultured phage genomes.…”