A comprehensive understanding of the processes associated with endosymbiosis is important for our knowledge of the evolution of eukaryotes. Investigations of the relatively recent secondary (and tertiary) endosymbioses of plastids (chloroplasts) could help us understand the processes behind the much more ancient primary endosymbiosis.
One of these endosymbioses (a case of serial secondary endosymbiosis) resulted in the replacement of the ancient peridinin-plastid by a green algal derived plastid in the dinoflagellate Lepidodinium chlorophorum. It was originally thought that this plastid was derived from an ancestor of the Prasinophyceae. Here, we demonstrate that this association is excluded in phylogenetic trees, and that the green plastid probably is derived from either the Trebouxiphyceae or the Ulvophyceae. In addition, the genome of the green plastid is likely quite reduced in genetic content, more than any other genomes found in green plastids.
The genomes of plastids do not code for all the proteins that are needed for the proper function of the plastid, most of these are encoded in the nuclear genome. These genes were transferred from the endosymbiont to the nuclear genome during the endosymbiosis. To be able to be transported back to the plastid, these proteins have a transit peptide added to their N-terminal. In secondary plastids, a signal peptide is also added to the N-terminal. The transit peptides of L. chlorophorum have characteristics which make them intermediate to the unusual transit peptides of K. veneficum and all other investigated species. Also, the signal peptides of L. chlorophorum have a hydrophilic part, which is not common among algae.