Size does matter – distinguishing bacteriophages by genome length (and ‘breadth’)

Abstract

Genome size and nucleic acid composition are basic characteristics of bacteriophages (phages). With larger genomes come increases in gene number, greater infection and virion sophistication, higher likelihood of gene acquisition via horizontal gene transfer (HGT), and additional genetic redundancy both within and between genomes (the latter referring to gene duplication and redundancy with host functions, respectively). Larger, that is, tailed phages in fact are among the most recombinogenic organisms on earth, often possessing numerous genes of mysterious function, many of which in at least some phages can be deleted without greatly impacting laboratory propagation. Larger phages, through the use of more sophisticated polymerases as well as proofreading and genome repair functions, also are less prone to replicative infidelities. As a consequence, their per-nucleotide mutation rates are substantially lower than those of smaller phages. Here, rather than macroevolutionary trends as typically considered from the perspective of comparative genomics, I emphasise instead microevolutionary processes, particularly the role of mutation as an immediate source of genetic variation within populations. Within this context I differentiate the viruses of domain Bacteria into four genome-size categories: very small (single-stranded RNA phages), small (single-stranded DNA phages), medium (lipid-containing, double-stranded DNA, tailless phages), and large, or at least larger (tailed phages).