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Plastids are known in both alveolates and euglenozoans to have been derived from secondary endosymbiosis: the uptake of a eukaryotic alga by another eukaryote. In the Euglenozoa, plastids are derived from a green alga and are relatively restricted, being found in a subset of euglenids and nowhere else, namely the “euglenophytes” (Leander, 2004). In the Alveolata, plastids are derived from a red alga and are more widespread and ancient, being known in dinoflagellates and apicomplexans, and suspected of originating before the divergence of alveolates (Keeling, 2009). As with nuclear genomes, plastids have evolved a number of unusual characteristics, some unique and some arising convergently. Euglenophyte plastid genomes are home to some unique self-splicing introns (Copertino and Hallick, 1993), whereas the dinoflagellate plastid genome has been massively reduced in coding content and broken into single gene minicircles with polyuridylylated transcripts (Wang and Morse, 2006). Curiously, both features are also found in kinetoplastid mitochondria (Lukeš et al., 2005).

Once again, however, 2 probably interconnected features have arisen in both groups. The vast majority of secondary plastids are bounded by 4 membranes. Most proteins in these plastids are encoded in the nucleus and are posttranslationally targeted to the organelle by way of a 2-part pathway beginning with the endomembrane system and followed by the original primary plastid targeting system. In dinoflagellates and euglenophytes, however, the plastid is novel in that it is bounded by 3 membranes rather than 4. It was argued that this may reflect a different mechanism of plastid uptake, specifically that in these lineages plastids arose through myzocytosis whereas other secondary plastids arose through endocytosis. Myzocytosis is a mode of predation where a cell pierces its prey and sucks the prey cytoplasm directly into a digestive vacuole, leaving the prey wall and membrane behind. Although not as common as endocytosis of whole prey cells, myzocytosis is known in both dinoflagellates and euglenozoans, leading to the suggestion that their plastids originated from a myzocytosed alga, and therefore lacked its plasma membrane (Schnepf and Deichgraber, 1984). However, plastids in the closest relatives of dinoflagellates, apicomplexans and Chromera, are bounded by 4 membranes and have now been shown to be orthologous to the dinoflagellate plastid (Oborník et al., 2009). Accordingly, in at least dinoflagellates, plastids must have originated in the same fashion as some 4-membrane counterparts and at one time been bounded by 4 membranes, which means that the origins of 3 membranes around the plastids in dinoflagellates and euglenophytes cannot be attributed to a shared, unusual mechanism such as myzocytosis.

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