Understanding genome complexity and protein evolution in ciliates: insights from mitchondria and nuclei

Abstract

We are exploring the evolutionary implications of genome duality in ciliates. Ciliates possess both a somatic macronucleus (MAC) and a germline micronucleus (MIC). Only the MAC is transcriptionally active, and divides by amitosis rather than mitosis and meiosis. We have previously hypothesized that genome duality is the driving force behind the heterogeneous and unusually elevated rates of amino acid substitutions we find in some protein coding genes. Does the dimorphic nature of the ciliate genome allow them to “cross the valleys in the adaptive landscape” of protein evolution? To test this hypothesis, we are analyzing additional protein genes as well as mitochondrial genes. Mitochondrial genes serve as an excellent comparison to those of the nucleus because phylogenetic information lost by the rapidly evolving nuclear genome may be retained in the mitochondria.