Getting Ready for the Era of Comparative Genomics: The Importance of Viruses

Viruses continue to provide clues to many biological processes that were not known only a few years ago. This chapter discusses the role of viruses (and virologists) in defining comparative genomics. The reasons why viruses have been popular as model systems are relatively simple: The number of genes in virus genomes is small, and the number of genetically homogeneous progeny that can be obtained in the laboratory is large. The combinatorial approach to classification (at least to virus classification) appears to produce a larger number of possibilities than are actually employed by nature. This results in many empty classes in Agol's scheme and in Koonin's classification. Apparently, the evolutionary process operates under constraints, so its results do not look like the product of indiscriminate mixing and matching. Perhaps every combinatorial classification should be expected to contain many empty classes. The auxiliary evidence strongly supported sequence similarities among the proteins conserved in RNA viruses: First, there was plenty of genetic data mapping replication ability to the RNA-dependent RNA polymerase (RdRp) domain. Second, conservation of gene order in virus genomes was observed in RNA viruses. The chapter also examines another line of comparative virus genomics—namely, the study of evolution of individual protein sequences.