Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

Abstract

Viruses are the most abundant biological entities on earth and encompass a vast amount of genetic diversity. The recent rapid increase in the number of sequenced viral genomes has created unprecedented opportunities for gaining new insight into the structure and evolution of the virosphere. Here, we present an update of the phage orthologous groups (POGs), a collection of 4,542 clusters of orthologous genes from bacteriophages that now also includes viruses infecting archaea and encompasses more than 1,000 distinct virus genomes. Analysis of this expanded data set shows that the number of POGs keeps growing without saturation and that a substantial majority of the POGs remain specific to viruses, lacking homologues in prokaryotic cells, outside known proviruses. Thus, the great majority of virus genes apparently remains to be discovered. A complementary observation is that numerous viral genomes remain poorly, if at all, covered by POGs. The genome coverage by POGs is expected to increase as more genomes are sequenced. Taxon-specific, single-copy signature genes that are not observed in prokaryotic genomes outside detected proviruses were identified for two-thirds of the 57 taxa (those with genomes available from at least 3 distinct viruses), with half of these present in all members of the respective taxon. These signatures can be used to specifically identify the presence and quantify the abundance of viruses from particular taxa in metagenomic samples and thus gain new insights into the ecology and evolution of viruses in relation to their hosts.

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

“…Integrases are highly ubiquitous, and can be shared by phages, whereas previous bioinformatic analysis (Kristensen et al 2013), found that many other functions are phage-specific (i.e. pertaining to phages, and not bacteria), including the large subunit of terminases, portal proteins, and structural proteins.…”

“…Those ORFs that returned more descriptive hits (as opposed to hypothetical, and including DNA helicases, DNA integrases, DNA polymerases, portal proteins, structural proteins and the large subunit of terminases), all belonged to proteins most prevalent in single-annotated phage genomes (Kristensen et al 2013) as opposed to those mined from metagenomic data. Integrases are highly ubiquitous, and can be shared by phages, whereas previous bioinformatic analysis (Kristensen et al 2013), found that many other functions are phage-specific (i.e.…”

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…Genetic mosaicism has been previously pointed out as a factor impeding meaningful classification of tailed bacteriophages (order Caudovirales) 54 . However, the coding capacity of tailed bacteriophages is typically large enough to accommodate a representative core gene set 55,56 sufficient for hierarchical clustering of these viruses into biologically significant subdivisions 57,58 . For viruses with small genomes, on the other hand, the effect of horizontal gene transfer on the 'identity' of a viral group is considerably more acute.…”

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

“…The gene repertoires of viruses are enormously diversified, with the great majority of the genes represented only in narrow groups of viruses (20,21). However, several "viral hallmark genes" that encode proteins responsible for key functions in virion formation and genome replication are shared by numerous, diverse viruses with different strategies of genome replication and expression (22) (Fig.…”