Gene content phylogeny of herpesviruses.

Clusters of orthologous groups [COGs; Tatusov, R. L., Koonin, E. V. & Lipman, D. J. (1997) Science 278, 631-637] were identified for a set of 13 completely sequenced herpesviruses. Each COG represented a family of gene products conserved across several herpes genomes. These families were defined without using an arbitrary threshold criterion based on sequence similarity. The COG technique was modified so that variable stringency in COG construction was possible. High stringencies identify a core set of highly conserved genes. Varying COG stringency reveals differences in the degree of conservation between functional classes of genes. The COG data were used to construct whole-genome phylogenetic trees based on gene content. These trees agree well with trees based on other methods and are robust when tested by bootstrap analysis. The COG data also were used to construct a reciprocal tree that clustered genes with similar phylogenetic profiles. This clustering may give clues to genes with related functions or with related histories of acquisition and loss during herpesvirus evolution.

[1]  Michael Y. Galperin,et al.  Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. , 1999, Genome research.

[2]  Michael Y. Galperin,et al.  Beyond complete genomes: from sequence to structure and function. , 1998, Current opinion in structural biology.

[3]  Roderic D. M. Page,et al.  TreeView: an application to display phylogenetic trees on personal computers , 1996, Comput. Appl. Biosci..

[4]  Doolittle Wf.  Phylogenetic Classification and the Universal Tree , 1999 .

[5]  D. Fischer,et al.  Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[6]  M. Craxton,et al.  The DNA sequence of human herpesvirus-6: structure, coding content, and genome evolution. , 1995, Virology.

[7]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[8]  George D. Rose,et al.  A protein taxonomy based on secondary structure , 1999, Nature Structural Biology.

[9]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[10]  S. Fitz-Gibbon,et al.  Whole genome-based phylogenetic analysis of free-living microorganisms. , 1999, Nucleic Acids Research.

[11]  P A Pevzner,et al.  Genome sequence comparison and scenarios for gene rearrangements: a test case. , 1995, Genomics.

[12]  B. Dujon,et al.  The genomic tree as revealed from whole proteome comparisons. , 1999, Genome research.

[13]  B. Snel,et al.  Genome phylogeny based on gene content , 1999, Nature Genetics.

[14]  A. Davison,et al.  Channel catfish virus: a new type of herpesvirus. , 1992, Virology.

[15]  E V Koonin.  The emerging paradigm and open problems in comparative genomics. , 1999, Bioinformatics.