Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts - PubMed (original) (raw)

Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts

David M Kristensen et al. J Bacteriol. 2011 Apr.

Abstract

We have identified conserved orthologs in completely sequenced genomes of double-strand DNA phages and arranged them into evolutionary families (phage orthologous groups [POGs]). Using this resource to analyze the collection of known phage genomes, we find that most orthologs are unique in their genomes (having no diverged duplicates [paralogs]), and while many proteins contain multiple domains, the evolutionary recombination of these domains does not appear to be a major factor in evolution of these orthologous families. The number of POGs has been rapidly increasing over the past decade, the percentage of genes in phage genomes that have orthologs in other phages has also been increasing, and the percentage of unknown "ORFans" is decreasing as more proteins find homologs and establish a family. Other properties of phage genomes have remained relatively stable over time, most notably the high fraction of genes that are never or only rarely observed in their cellular hosts. This suggests that despite the renowned ability of phages to transduce cellular genes, these cellular "hitchhiker" genes do not dominate the phage genomic landscape, and a large fraction of the genes in phage genomes maintain an evolutionary trajectory that is distinct from that of the host genes.

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Figures

Fig. 1.

Fig. 1.

Method of POG construction. The earlier POGs (at left) were built from proteins in phages, whereas in this study we added (at right) the joining of closely related isolates (based on shared genes) and splitting proteins into their component domains.

Fig. 2.

Fig. 2.

Effect of BLAST E-value threshold on POGs (a) and OrthoMCL groups (b). Left axes, numbers of groups; right axes, numbers of proteins in groups.

Fig. 3.

Fig. 3.

Distribution of phageness quotient according to the number of proteins in a POG (a) and the number of POGs (b).

Fig. 4.

Fig. 4.

Properties of dsDNA phage genomes over the past decade. (a) Numbers of genomes and POGs; (b) total number of proteins in genomes and number that are in POGs; (c) percentage of those proteins in or not in POGs.

Fig. 5.

Fig. 5.

(a) Percentage of POGs that are never or very rarely observed in their cellular hosts (PQ = infinity) or that have homologs in at least 2 orders of magnitude more phage species than host ones (PQ ≥ 2). (b) Overall number of phage and host (prokaryotic) genomes available at the end of each year.

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