Reduced and lost plastid genomes

As outlined above, plastid loss obviously does not occur easily, even in organisms that have lost their photosynthetic capability. Nevertheless, individual plastid losses have been described in strameno-piles, euglenophytes, and in dinoflagellates (Cavalier-Smith et al. 1995; Preisfeld et al. 2001; Saldarriaga et al. 2001).

Phylogenetic analyses indicated that dino-flagellates, apicomplexa, and ciliates are mono-phyletic and are therefore grouped together as alveolates (e.g. Van de Peer et al. 1996; Fast et al. 2001; Cavalier-Smith 2003). Because dino-flagellates and apicomplexa harbor remnant plas-tids of most likely red algal origin, it is self-evident to speculate about a loss of plastids in ciliates. The same might be true for the stramenopile-related oomycetes, which lack plastids (Stoebe and Maier 2002). However, for all of these examples, inferences from early branching lineages in phyloge-netic trees are complicated and might lead to inaccurate predictions of plastid loss. Moreover, vestigal plastids may be overlooked, as indicated in the case of some stramenopiles (Sekiguchi et al. 2002).

Assuming that complete loss of plastids is possible, one can predict that other plastid-less lines had a phototrophic history. To identify such groups, the study of cyanobacterial genes known to have displaced their cytosolic counterparts is of major interest. One of these ''marker'' genes is the enzyme 6-phosphogluconate dehydrogenase (gnd), which was transferred to the nuclear genome in embryophytes and displaced the cytosolic copy after duplication (Krepinsky et al. 2001). Therefore, gnd is indeed a good indicator for the evaluation of a phototrophic history of hetero-trophic organisms. Using this marker gene, phylogenetic analyses indicated that the human blood-stream parasite Trypanosoma brucei, which is closely related to the photosynthetically-active euglenophyte Euglena gracilis, possesses a gnd gene of cyanobacterial origin and might therefore be secondarily non-photosynthetic (Krepinsky et al. 2001; Martin and Borst 2003). In other studies, Andersson and Roger (2002) discovered that oomycetes and some heteroloboseid amoebo-flagellates harbor cyanobacterial gnd genes, too; a lateral gene transfer event might explain these results. Alternatively, the gnd phylogeny could indicate that these organisms once harbored plas-tids of primary or secondary origin. If the latter is true, more genes of cyanobacterial origin should be found in ongoing genome projects.

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