Although the collection of completely sequenced mitochondrial genomes is expanding rapidly, only recently has a phylogenetically broad representation of mtDNA sequences from protists (mostly unicellular eukaryotes) become available. This review surveys the 23 complete protist mtDNA sequences that have been determined to date, commenting on such aspects as mitochondrial genome structure, gene content, ribosomal RNA, introns, transfer RNAs and the genetic code and phylogenetic implications. We also illustrate the utility of a comparative genomics approach to gene identification by providing evidence that orfB in plant and protist mtDNAs is the homolog of atp8 , the gene in animal and fungal mtDNA that encodes subunit 8 of the F0portion of mitochondrial ATP synthase. Although several protist mtDNAs, like those of animals and most fungi, are seen to be highly derived, others appear to be have retained a number of features of the ancestral, proto-mitochondrial genome. Some of these ancestral features are also shared with plant mtDNA, although the latter have evidently expanded considerably in size, if not in gene content, in the course of evolution. Comparative analysis of protist mtDNAs is providing a new perspective on mtDNA evolution: how the original mitochondrial genome was organized, what genes it contained, and in what ways it must have changed in different eukaryotic phyla.

The mitochondrial DNA (mtDNA) of Porphyra purpurea, a circular-mapping genome of 36,753 bp, has been completely sequenced. A total of 57 densely packed genes has been identified, including the basic set typically found in animals and fungi, as well as seven genes characteristic of protist and plant mtDNAs and specifying ribosomal proteins and subunits of succinate:ubiquinone oxidoreductase. The mitochondrial large subunit rRNA gene contains two group II introns that are extraordinarily similar to those found in the cyanobacterium Calothrix sp, suggesting a recent lateral intron transfer between a bacterial and a mitochondrial genome. Notable features of P. purpurea mtDNA include the presence of two 291-bp inverted repeats that likely mediate homologous recombination, resulting in genome rearrangement, and of numerous sequence polymorphisms in the coding and intergenic regions. Comparative analysis of red algal mitochondrial genomes from five different, evolutionarily distant orders reveals that rhodophyte mtDNAs are unusually uniform in size and gene order. Finally, phylogenetic analyses provide strong evidence that red algae share a common ancestry with green algae and plants.

The mitochondrial DNA (mtDNA) of Porphyra purpurea , a circular-mapping genome of 36,753 bp, has been completely sequenced. A total of 57 densely packed genes has been identified, including the basic set typically found in animals and fungi, as well as seven genes characteristic of protist and plant mtDNAs and specifying ribosomal proteins and subunits of succinate:ubiquinone oxidoreductase. The mitochondrial large subunit rRNA gene contains two group II introns that are extraordinarily similar to those found in the cyanobacterium Calothrix sp, suggesting a recent lateral intron transfer between a bacterial and a mitochondrial genome. Notable features of P. purpurea mtDNA include the presence of two 291-bp inverted repeats that likely mediate homologous recombination, resulting in genome rearrangement, and of numerous sequence polymorphisms in the coding and intergenic regions. Comparative analysis of red algal mitochondrial genomes from five different, evolutionarily distant orders reveals that rhodophyte mtDNAs are unusually uniform in size and gene order. Finally, phylogenetic analyses provide strong evidence that red algae share a common ancestry with green algae and plants. INTRODUCTIONHistorically considered to be "red plants," red algae (rhodophytes) were grouped together with protists only in the middle of this century; however, debate continues as to when this taxonomic group first appeared in the evolutionary history of mitochondria-containing eukaryotes. Because the red algal cell lacks flagellar basal bodies and centrioles, some workers have claimed that rhodophytes are the most early diverging and primitive group among photosynthetic eukaryotes (e.g., Lee, 1989). This view also has been suggested by certain molecular phylogenies (e.g., Lipscomb, 1989;Stiller and Hall, 1997). Some authors even advocate that red algae, in particular Cyanidioschyzon spp and Cyanidium spp, represent the evolutionary bridge between cyanobacteria and eukaryotes (Seckbach, 1994). An opposite interpretation contends that the red algae represent a derived group that has secondarily lost many of the distinctive features of the protistan cytoskeleton (Pueschel, 1990;Scott and Broadwater, 1990). Finally, it has been proposed that red algae may have given rise to the fungi (Demoulin, 1985) or that red algae are affiliated with the plant kingdom via common ancestry with green algae (see, e.g., Bhattacharya et al., 1993; Cavalier-Smith, 1993;McFadden et al., 1994;Schlegel, 1994;Paquin et al., 1997;Lang et al., 1998). This broad spectrum of coexisting, mutually exclusive hypotheses highlights our limited knowledge about the phylogenetic relationship between rhodophytes and other eukaryotic phyla.Rhodophytes form a morphologically heterogeneous phylum that has more species ( ‫ف‬ 2500 to 6000 in at least 12 orders; Woelkerling, 1990) than all other seaweeds combined. Multicellular as well as unicellular rhodophyte genera exist, and there is also considerable variety in morphology and physiology throughout the phylum. On the basis...