A phylogenetic comparison of gene trees constructed from plastid, mitochondrial and genomic DNA of Plasmodium species

Gene trees of Plasmodium species have been reported, for the nuclear encode d genes (e.g. the Small Subunit rRNA) and a mitochondrial encoded gene, cyt ochrome b. Here, we have analyzed a plastid gene coding for caseinolytic pr otease ClpC, whose structure, function and evolutionary history have been s tudied in various organisms. This protein possesses a 220-250 amino acid lo ng AAA domain (ATPases associated with a variety of cellular activities) th at belongs to the Walker super family of ATPases and GTPases. We have seque nced the AAA motif of this gene, encoding the protein from nine different s pecies of Plasmodium infecting rodents, birds, monkeys, and humans. The cod on usage and GC content of each gene were nearly identical in contrast to t he widely varying nucleotide composition of genomic DNAs. Phylogenetic tree s derived from both DNA and inferred protein sequences have consistent topo logies. We have used the ClpC sequence to analyze the phylogenetic relation ship among Plasmodium species and compared it with those derived from mitoc hondrial and genomic sequences. The results corroborate well with the trees constructed using the mitochondrially encoded cytochrome b. However, an im portant element distinguishes the trees: the placement of Plasmodium elonga tum near the base of the plastid tree, indicating an ancient lineage of par asites in birds that branches from the tree prior to other lineages of avia n malaria and the human parasite, P. falciparum (C) 2001 Elsevier Science B .V. All rights reserved.