Bacteriophages and their genomes

Abstract

Bacteriophages occupy a unique position in biology, representing an absolute majority of all organisms in the biosphere. Because their genomes are relatively small, elucidating the genetic diversity of the phage population, deciphering their origins, and identifying the evolutionary mechanisms that shape the population would seem readily feasible. And yet the pace of phage genome characterization has slowed over the past three years, reflecting in part a need to transition from sequencing known and well-characterized bacteriophages to the isolation and comparative analysis of new isolates. The current state of bacteriophage genomics shows that the genetic diversity of the population is very high, that phages have been actively evolving for billions of years with active engagement of horizontal genetic exchange, and that their genomes are consequently pervasively mosaic in their architectures. But we have barely scratched the surface and the next years of phage genome exploration promise to be especially revealing.

Phylogenomic Network and Comparative Genomics Reveal a Diverged Member of the ϕKZ-Related Group, Marine Vibrio Phage ϕJM-2012

“…However, this does not necessarily indicate the presence of nonhomologous or illegitimate recombination, since it could be explained by the presence of relatively short and little-known conserved sequences at the gene boundaries (19,60) and the lack of information on intermediate-sequence similarities (60). Thus, it is difficult to explicitly determine the genetic mechanisms of this recombination (19,60). Nevertheless, on the basis of the presence of relevant genes, we propose that all types of recombination (illegitimate, homologous, and site specific) are likely to be responsible for the mosaic architecture of the JM-2012 genome.…”

“…Thus, classical taxonomic classification has proven difficult, often limiting our understanding of the genomic diversity and evolution of phages (18,19). As a promising approach, recent studies have proposed reticulated network modeling, in which pairwise relationships of phage genomes are represented as weighted phage-phage similarities in terms of gene/ protein contents (15,20).…”

Virus taxonomy in the age of metagenomics

“…Frameworks of this kind may have to be tailored to the virus group. For example, bacteriophage taxonomy is typically based on virion sequence and structure 58 , but these characteristics may not be appropriate for the classification of animal and plant RNA viruses, in which deeper relationships are most often apparent in the gene sequences of the RNA polymerase and other conserved replication-associated proteins 59 .…”

Molecular architecture of tailed double-stranded DNA phages

“…2,31,32 DNA of some phages, contains modified nucleotides, which helps to protect the genomes against nuclease degradation. For instance, chromosomes of T-even phages contain glucosylated hydroxymethylcytosine residues.…”