Genomic studies of the evolution of haptophytes and dinoflagellates with emphasis on the chromalveolate hypothesis

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All photosynthetic eukaryotes rely, partially or totally, on their plastids to live. The plastids, which ultimately are highly modified cyanobacteria, were acquired through a process of primary, secondary, or tertiary endosymbiosis. Four photosynthetic lineages, including haptophytes, dinoflagellates, cryptophytes, and heterokonts, contain secondary plastids with chlorophyll c as a main photosynthetic pigment. These four lineages were grouped together, along with their heterotrophic relatives, on the basis of their pigmentation and called chromalveolates by Cavalier-Smith. However, the phylogenetic relationships among these algae are unknown and the chromalveolate hypothesis remains very controversial. This study focuses on increasing the amount of genomic data from a poorly studied chromalveolate lineage, the haptophytes, and understanding plastid evolution in chromalveolates. Both the chloroplast and mitochondrial genomes of the haptophyte <em>Emiliania huxleyi</em> were sequenced and examined to describe basic genomic properties, as well as perform comparative studies. Phylogenetic analyses, including data acquired from haptophytes, support a monophyletic chl c containing plastid clade derived from the red algae, after the divergence of Cyanidiales, with the cryptophyte plastid basal or sister to the haptophyte plastid. In addition, phylogenetic analyses using mitochondrial data suggest a relationship of haptophytes and cryptophytes. The chromalveolate clade as a whole is not recovered nor rejected by the data. Analysis of an EST project from the heterotrophic dinoflagellate <em>Crypthecodinium cohnii</em> indicates that <em>C. cohnii</em> is not only derived from a photosynthetic ancestor, but very likely retains a non-photosynthetic plastid. Analyses of putative gene function suggest that heme biosynthesis, non-mevalonate isoprenoid biosynthesis, amino-acid metabolism, and Fe-S cluster assembly may occur in the plastid. These observations are also consistent with the chromalveolate hypothesis, which proposes that several major groups of eukaryotes, including alveolates, haptophytes, cryptophytes, and heterokonts, may form a monophyletic group with a photosynthetic common ancestor, and that nonphotosynthetic members are secondarily so.