  Gene duplication is key to molecular evolution in all three domains of life
and may be the first step in the emergence of new gene function. It is a well
recognized feature in large DNA viruses, but has not been studied extensively
in the largest known virus to date, the recently discovered Acanthamoeba
Polyphaga Mimivirus. Here we present a systematic analysis of gene and genome
duplication events in the Mimivirus genome. We find that one third of the
Mimivirus genes are related to at least one other gene in the Mimivirus genome,
either through a large segmental genome duplication event that occurred in the
more remote past, either through more recent gene duplication events, which
often occur in tandem. This shows that gene and genome duplication played a
major role in shaping the Mimivirus genome. Using multiple alignments together
with remote homology detection methods based on Hidden Markov Model comparison,
we assign putative functions to some of the paralogous gene families. We
suggest that a large part of the duplicated Mimivirus gene families are likely
to interfere with important host cell processes, such as transcription control,
protein degradation, and cell regulatory processes. Our findings support the
view that large DNA viruses are complex evolving organisms, possibly deeply
rooted within the tree of life, and oppose the paradigm that viral evolution is
dominated by lateral gene acquisition, at least in what concerns large DNA
viruses.
