Phylogenetic affinities of Diplonema within the euglenozoa as inferred from the SSU rRNA gene and partial COI protein sequences

In order to shed light on the phylogenetic position of diplonemids within t he phylum Euglenozoa, we have sequenced small subunit rRNA (SSU rRNA) genes from Diplonema (syn, Isonema) papillatum and Diplonema sp, We have also an alyzed a partial sequence of the mitochondrial gene for cytochrome c oxidas e subunit I from D. papillatum. With both markers, the maximum likelihood m ethod favored a closer grouping of diplonemids with kinetoplastids, while t he parsimony and distance suggested a closer relationship of diplonemids wi th euglenoids, In each case, the differences between the best tree and the alternative trees were small. The frequency of codon usage in the partial D . papillatum COI was different from both related groups; however, as is the case in kinetoplastids but not in Euglena, both the non-canonical UGA codo n and the canonical UGG codon were used to encode tryptophan in Diplonema.