HSP90, tubulin and actin are retained in the tertiary endosymbiont genome of Kryptoperidinium foliaceum.

The dinoflagellate Kryptoperidinium foliaceum has replaced its ancestral peridinin-containing plastid with a fucoxanthin-containing diatom plastid via tertiary endosymbiosis. The diatom endosymbiont of K. foliaceum is much less reduced than well-studied endosymbiotic intermediates, such as cryptophytes and chlorarachniophytes, where relict nuclear genomes are retained in secondary endosymbionts. The K. foliaceum endosymbiont retains a prominent nucleus, multiple four-membrane plastids, and mitochondria, all within a relatively large volume of cytoplasm that is separated from the host cytoplasm by a single membrane. Here we report the first protein-coding gene sequences from the K. foliaceum endosymbiont and host nuclear genomes. We have characterised genes for nucleus-encoded cytosolic proteins, actin (from endosymbiont), alpha-tubulin (from both), beta-tubulin (from host), and HSP90 (from both), in addition to homologues from pennate diatoms Nitzschia thermalis and Phaeodactylum tricornutum. Phylogenetic reconstruction shows that the actin is diatom-derived, the beta-tubulin dinoflagellate-derived, while both diatom- and dinoflagellate-derived alpha-tubulin and HSP90 genes were found. The base composition biases of these genes co-varied with their phylogenetic position, suggesting that the genes still reside in their respective genomes. The presence of these genes implies they are still functional and more generally indicates that the endosymbiont is less genetically reduced than those of cryptophytes or chlorarachniophytes, raising the interesting question of whether any genes have transferred between the two nuclear genomes.

Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage.

Oxyrrhis marina and Perkinsus marinus are two alveolate species of key taxonomic position with respect to the divergence of apicomplexans and dinoflagellates. New sequences from Oxyrrhis, Perkinsus and a number of dinoflagellates were added to datasets of small-subunit (SSU) rRNA, actin, alpha-tubulin and beta-tubulin sequences, as well as to a combined dataset of all three protein-coding genes, and phylogenetic trees were inferred. The parasitic Perkinsus marinus branches at the base of the dinoflagellate clade with high support in most of the individual gene trees and in the combined analysis, strongly confirming the position originally suggested in previous SSU rRNA and actin phylogenies. The SSU rRNA from Oxyrrhis marina is extremely divergent, and it typically branches with members of the Gonyaulacales, a dinoflagellate order where SSU rRNA sequences are also divergent. Conversely, none of the three protein-coding genes of Oxyrrhis is noticeably divergent and, in trees based on all three proteins individually and in combination, Oxyrrhis branches at the base of the dinoflagellate clade, typically with high bootstrap support. In some trees, Oxyrrhis and Perkinsus are sisters, but most analyses indicate that Perkinsus diverged prior to Oxyrrhis. Morphological characters have previously pointed to Oxyrrhis as an early branch in the dinoflagellate lineage; our data support this suggestion and significantly bolster the molecular data that support a relationship between Perkinsus and dinoflagellates. Together, these two organisms can be instrumental in reconstructing the early evolution of dinoflagellates and apicomplexans by helping to reveal aspects of the ancestors of both groups.