Data from: Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

Microbes and their viruses drive myriad processes across ecosystems
ranging from oceans and soils to bioreactors and humans. Despite this
importance, microbial diversity is only now being mapped at scales
relevant to nature, while the viral diversity associated with any
particular host remains little researched. Here we quantify
host-associated viral diversity using viral-tagged metagenomics, which
links viruses to specific host cells for high-throughput screening and
sequencing. In a single experiment, we screened 107 Pacific Ocean viruses
against a single strain of Synechococcus and found that naturally
occurring cyanophage genome sequence space is statistically clustered into
discrete populations. These population-based, host-linked viral ecological
data suggest that, for this single host and seawater sample alone, there
are at least 26 double-stranded DNA viral populations with estimated
relative abundances ranging from 0.06 to 18.2%. These populations include
previously cultivated cyanophage and new viral types missed by decades of
isolate-based studies. Nucleotide identities of homologous genes mostly
varied by less than 1% within populations, even in hypervariable genome
regions, and by 42–71% between populations, which provides benchmarks for
viral metagenomics and genome-based viral species definitions. Together
these findings showcase a new approach to viral ecology that
quantitatively links objectively defined environmental viral populations,
and their genomes, to their hosts.