Gene content phylogeny of herpesviruses

Clusters of orthologous groups [COGs; Tatusov, R. L., Koonin, E. V. & Lipma n, D. J. (1997) Science 278, 631-637] were identified for a set of 13 compl etely sequenced herpesviruses. Each COG represented a family of gene produc ts conserved across several herpes genomes. These families were defined wit hout using an arbitrary threshold criterion based on sequence similarity. T he COG technique was modified so that variable stringency in COG constructi on was possible. High stringencies identify a core set of highly conserved genes. Varying COG stringency reveals differences in the degree of conserva tion between functional classes of genes. The COG data were used to constru ct whole-genome phylogenetic trees based on gene content. These trees agree well with trees based on other methods and are robust when tested by boots trap analysis. The COG data also were used to construct a reciprocal tree t hat clustered genes with similar phylogenetic profiles. This clustering may give clues to genes with related functions or with related histories of ac quisition and loss during herpesvirus evolution.