A phylogenetic assessment of the eukaryotic light-harvesting antenna proteins, with implications for plastid evolution

The light-harvesting complexes (LHCs) are a superfamily of chlorophyll-bind ing proteins present in all photosynthetic eukaryotes. The Lhc genes are nu clear-encoded, yet the pigment-protein complexes are localized to the thyla koid membrane and provide a marker to follow the evolutionary paths of plas tids with different pigmentation. The LHCs are divided into the chlorophyll a/b-binding proteins of the green algae, euglenoids, and higher plants and the chlorophyll a/b-binding proteins of various algal taxa. This work exam ines the phylogenetic position of the LHCs from three additional taxa: the rhodophytes, the cryptophytes, and the chlorarachniophytes. Phylogenetic an alysis of the LHC sequences provides strong statistical support for the clu stering of the rhodophyte and cryptomonad LHC sequences within the chloroph yll a/c-binding protein lineage, which includes the fucoxanthin-chlorophyll proteins (FCP) of the heterokonts and the intrinsic peridinin-chlorophyll proteins (iPCP) of the dinoflagellates, These associations suggest that pla stids from the heterokonts, haptophytes, cryptomonads, and the dinoflagella te, Amphidinium, evolved from a red algal-like ancestor. The Chlorarachnion LHC is part of the chlorophyll a/b-binding protein assemblage, consistent with pigmentation, providing further evidence that its plastid evolved from a green algal secondary endosymbiosis. The Chlorarachnion LHC sequences cl uster with the green algal LHCs that are predominantly associated with phot osystem II (LHCII). This suggests that the green algal endosymbiont that ev olved into the Chlorarachnion plastid was acquired following the emergence of distinct LHCI and LHCII complexes.