LOCATION OF PROTIST LINEAGES IN A PHYLOGENETIC TREE INFERRED FROM SEQUENCES OF DNA-DEPENDENT RNA-POLYMERASES

The nearly complete sequence of the gene encoding the largest component of the DNA-dependent RNA polymerase-2 from the amitochondrial diplomonad Giardia lamblia is reported. The position of Giardia and other deep branching protists within a phylogenetic tree containing all completely or partially known eukaryotic RNA polymerases-1,-2, and -3A-component sequences and some homologous archaeal (archaebacterial) and bacterial (eubacterial) outgroup-sequences has been inferred by parsimony and distance methods. A consensus tree has been concluded from the branching orders of the most parsimonious and the least squares tree by fixing the costs of branch swapping to corresponding positions of the differing lineages in both trees. A 96% confidence value determined by a bootstrapping analysis based on the protein distance method clearly supported the fixation of Giardia as the deepest offshoot within the RNA polymerases-2 subtree, followed by the protists Trypanosoma brucei, Plasmodium falciparum and Euplotes octocarinatus. An internal branch, which separates the lineages of the eukaryotic polymerases-2 and -3 and the archaeal polymerases from those of the eukaryotic polymerases-1 and the bacterial polymerases, was found to be strongly supported by the result of the maximum parsimony inference. This branch, which can be considered to be an indicator for the chimeric origin of the eukaryotic nucleus, could not be confirmed in a distance analysis.