CONSERVED VIRUS PROTEIN FAMILIES IN BACTERIOPHAGE GENOMES AND IN METAGENOMES OF HUMANS

Abstract

Viruses are likely to be the most abundant genomes in the biosphere, displaying remarkable molecular diversity. Their fast-evolving genomes and lack of universal marker genes make phylogenetic and taxonomic studies more difficult than with other organisms. A detailed determination of gene conservation between virus genomes should facilitate the study of virus evolution and function. Here we used sequence similarity methods to build a phage orthologous groups (POGs) resource. The number of POGs has grown significantly in the past decade, while the percentage of genes in phage genomes that have orthologs in other phages has also been increasing, and the percentage of unknown "ORFans" - phage genes that are not in POGs - is decreasing. Other properties of phage genomes remain stable, in particular the high fraction of genes that are never or only rarely observed in their cellular hosts. This suggests that despite the role of phages in transferring cellular genes, a large fraction of the genes in phage genomes maintain an evolutionary trajectory that is distinct from that of host genes. Next generation sequencing technologies provide new opportunities to study viruses, their diversity and evolution, directly from environmental samples. The standards of sensitivity and specificity appropriate for analysis of these relatively short shotgun sequence reads are still evolving. In another part of our work, we used sensitive sequence similarity methods to identify more than 400 virus-related genes in 3,280 libraries derived from patients and environmental samples after low-complexity reads were removed. These identifications serve as a starting point to isolate viruses potentially associated with disease and outbreaks of unknown etiology.