The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage

The discovery of a non-photosynthetic plastid genome in Plasmodium falcipar um and other apicomplexans has provided a new drug target, but the evolutio nary origin of the plastid has been muddled by the lack of characters, that typically define major plastid lineages. To clarify the ancestry of the pl astid, we undertook a comprehensive analysis of all genomic characters shar ed by completely sequenced plastid genomes. Cladistic analysis of the patte rn of plastid gene loss and gene rearrangements suggests that the apicomple xan plastid is derived from an ancestor outside of the green plastid lineag e. Phylogenetic analysis of primary sequence data (DNA and amino acid chara cters) produces results that are generally independent of the analytical me thod, but similar genes (i.e. rpoB and rpoC) give similar topologies. The c onflicting phylogenies in primary sequence data sets make it difficult to d etermine the exact origin of the apicomplexan plastid and the apparent arti factual association of apicomplexan and euglenoid sequences suggests that D NA sequence data may be an inappropriate set of characters to address this phylogenetic question. At present we cannot reject our null hypothesis that the apicomplexan plastid is derived from a shared common ancestor between apicomplexans and dinoflagellates. During the analysis, we noticed that the Plasmodium tRNA-Met is probably tRNA-fMet and the tRNA-fMet is probably tR NA-Ile. We suggest that P. falciparum has lost the elongator type tRNA-Met and that similar to metazoan mitochondria there is only one species of meth ionine tRNA. In P. falciparum, this has been accomplished by recruiting the Net-type tRNA to dually function in initiation and elongation. The tRNA-Il e has an unusual stem-loop in the variable region. The insertion in this re gion appears to have occurred after the primary origin of the plastid and f urther supports the monophyletic ancestory of plastids.