The chlorophyll c-containing algae comprise four major lineages: dinoflagellates, haptophytes, heterokonts, and cryptophytes. These four lineages have sometimes been grouped together based on their pigmentation, but cytological and rRNA data had suggested that they were not a monophyletic lineage. Some molecular data support monophyly of the plastids, while other plastid and host data suggest different relationships. It is uncontroversial that these groups have all acquired plastids from another eukaryote, probably from the red algal lineage, in a secondary endosymbiotic event, but the number and sequence of such event(s) remain controversial. Understanding chlorophyll c-containing plastid relationships is a first step towards determining the number of endosymbiotic events within the chromalveolates. We report here phylogenetic analyses using 10 plastid genes with representatives of all four chromalveolate lineages. This is the first organellar genomescale analysis to include both haptophytes and dinoflagellates. Concatenated analyses support the monophyly of the chlorophyll c-containing plastids and suggest that cryptophyte plastids are the basal member of the chlorophyll c-containing plastid lineage. The gene psbA, which has at times been used for phylogenetic purposes, was found to differ from the other genes in its placement of the dinoflagellates and the haptophytes, and in its lack of support for monophyly of the green and red plastid lineages. Overall, the concatenated data are consistent with a single origin of chlorophyll c-containing plastids from red algae. However, these data cannot test several key hypothesis concerning chromalveolate host monophyly, and do not preclude the possibility of serial transfer of chlorophyll c-containing plastids among distantly related hosts.

Ribosome inactivating proteins are enzymes that depurinate a specific adenine residue in the alpha-sarcin-ricin loop of the large ribosomal RNA, being ricin and Shiga toxins the most renowned examples. They are widely distributed in plants and their presence has also been confirmed in a few bacterial species. According to this taxonomic distribution, the current model about the origin and evolution of RIP genes postulates that an ancestral RIP domain was originated in flowering plants, and later acquired by some bacteria via horizontal gene transfer. Here, we unequivocally detected the presence of RIP genes in fungi and metazoa. These findings, along with sequence and phylogenetic analyses, led us to propose an alternative, more parsimonious, hypothesis about the origin and evolutionary history of the RIP domain, where several paralogous RIP genes were already present before the three domains of life evolved. This model is in agreement with the current idea of the Last Universal Common Ancestor (LUCA) as a complex, genetically redundant organism. Differential loss of paralogous genes in descendants of LUCA, rather than multiple horizontal gene transfer events, could account for the complex pattern of RIP genes across extant species, as it has been observed for other genes.

The complete nucleotide sequence of the plastid genome of the haptophyte Emiliania huxleyi has been determined. E. huxleyi is the most abundant coccolithophorid and has a key role in the carbon cycle. It is also implicated in the production of dimethylsulphide (DMS), which is involved in cloud nucleation and may affect the global climate. Here, we report the plastid genome sequence of this ecologically and economically important species and compare its gene content and arrangement to other known plastid genomes. The genome is circular and consists of 105,309 bp with an inverted repeat of 4,841 bp. In terms of both genome size and gene content E. huxleyi cpDNA is substantially smaller than any other from the red plastid lineage. The genetic information is densely packed, with 86.8% of the genome specifying 110 identified protein-coding genes, 9 open reading frames, 28 different tRNAs, and 3 rRNAs. A detailed comparison to other plastid genomes, based on gene content, gene function, and gene cluster analysis is discussed. These analyses suggest a close relationship of the E. huxleyi cpDNA to the chlorophyll c-containing plastids from heterokonts and cryptophytes, and they support the origin of the chromophyte plastids from the red algal lineage.

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