Data from: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

The ecological importance of viruses is now widely recognized, yet our
limited knowledge of viral sequence space and virus-host interactions
precludes accurate prediction of their roles and impacts. Here we mined
publicly available bacterial and archaeal genomic datasets to identify
12,498 high‑confidence viral genomes linked to their microbial hosts.
These data augment public datasets 10-fold, provide first viral sequences
for 13 new bacterial phyla including ecologically abundant phyla, and help
taxonomically identify 7-38% of 'unknown' sequence space in
viromes. Genome- and network-based classification was largely consistent
with accepted viral taxonomy and suggested that (i) 264 new viral genera
were identified (doubling known genera) and (ii) cross-taxon genomic
recombination is limited. Further analyses provided empirical data on
extrachromosomal prophages and co‑infection prevalences, as well as
evaluation of in silico virus-host linkage predictions. Together these
findings illustrate the value of mining viral signal from microbial
genomes.