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Getting Ready for the Era of Comparative Genomics: The Importance of Viruses
#MMPMIDC7173418
Mushegian AR
Foundations of Comparative Genomics
2007[]; ? (?): 33-50
PMIDC7173418
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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.
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