The Phage Proteomic Tree: a genome-based taxonomy for phage

Abstract

There are approximately 10(31) phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage biodiversity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the "Phage Proteomic Tree," which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage biodiversity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage.

FIG. 1.

Rank abundance curve showing the number of significant similarities between each predicted phage protein against all other predicted phage proteins, as determined by BLASTP with an E-value cutoff of <0.1.

FIG. 2.

The Phage Proteomic Tree was constructed from 105 completely sequenced phage genomes. The tree was generated from length-corrected protein distance scores with a penalty of 10 for missing proteins as described in the text. Each phage genome is colored according to its ICTV classification as shown in the key. To make the figure easier to read, the large group of siphophage has been manually shifted away from the other phage groups. The dotted line indicates where the two groups would connect.