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Although thanks to the number of membranes surrounding the apicoplast
it was evident that it is a complex plastid originating from an at least secondary
endosymbiotic event (
K
¨
hler et al., 1997; McFadden et al., 1996
), its partic-
ular origin from within the green or red plastid lineage had remained
unknown for a long time. So far, only two groups of algae with secondary
green plastid are known, namely, the photosynthetic Euglenophyta and Chlo-
rarachniophyta, belonging to the excavates and rhizarians, respectively. Both
protist groups are supposed to have acquired their plastids relatively recently
(
Archibald, 2012
). All the other groups of algae known to harbor secondary
plastids, such as Stramenopila, Alveolata, Cryptophyta, and Haptophyta,
obtained them via the endosymbiotic relationship with a red alga. However,
even within dinoflagellates, a species-rich group of alveolate algae mostly
possessing a secondary red plastid, two species (
Lepidodinium viride
and
L. chlorophorum
) with the green secondary plastid have been described
(
Takishita et al., 2008; Watanabe et al., 1990
). Before the discovery of
chromerids (
Moore et al., 2008
), the dinoflagellates represented, due to their
sister position to the Apicomplexa, the closest known phototrophic relatives
of these obligatory parasites (
Zhang et al., 2000
). Unfortunately, since the
apicoplast lost all its photosynthetic functions and since the genome of the
dinoflagellate peridinin-pigmented plastid was reduced to an extremely nar-
row set of photosynthetic genes (
Barbrook and Howe, 2000; Green, 2004;
Zhang et al., 1999
), the plastid genomes of these related alveolates virtually
do not overlap (
Keeling, 2008
) and are, hence, beyond meaningful compar-
ison. The only genes shared by both groups are those coding for rRNAs;
however, their extreme AT richness and divergence make a trustable phylo-
genetic analysis highly questionable (
Dacks et al., 2002
;
Howe, 1992;
Oborn´k et al., 2002; Zhang et al., 2000
). Consequently, numerous phyloge-
netic analyses of the apicoplast genes led to contradictory results. While the
tufA
gene-based analyses supported the origin of the apicoplast from within
the green lineage (
Egea and LangUnnasch, 1995; K¨hler et al., 1997
), other
authors suggested its origin outside of the green lineage (
Blanchard and Hicks,
1999
) or inside the red plastid lineage (
Williamson et al., 1994
). The latter
origin is further supported by the structure of the super plastid operon of
the apicoplast genome, gene synteny, which is homologous to the red rather
than the green plastid genomes (
Blanchard and Hicks, 1999; McFadden and
Waller, 1997; Stoebe and Kowallik, 1999; Zhang et al., 2000
). In spite of that,
the green scenario came once more into the game, when the uniquely split
cox2 genes were found in the nuclear genomes of both apicomplexans and
leguminous plants (
Funes et al., 2002
). However, other researchers have
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