Those observations together with results obtained here suggest these isolates represent lineages that have undergone independent chloroplast reduction/degeneration. Curiously, although nuclear rDNA sequences do vary among Esoptrodinium isolates, that of isolate RP is identical (including the entire ITS1-5.8S-ITS2 region) to several clearly
chloroplast-bearing isolates (Fawcett and Parrow 2012). This suggests that the (presumably nonfunctional, below) psbA variant sequenced here has either occurred relatively recently (if RP represents a cryptic biological species independent from functional chloroplast-bearing isolates), or exists ATR activation as a plastid allele within a recombining nuclear rDNA clade that also contains apparently functional psbA alleles. Either case would be novel in dinoflagellates. Plastid reduction and/or loss may be common within dinoflagellates relative to other protist
groups (Saldarriaga et al. 2001), but plastid genetic and functional degeneration within a dinoflagellate morphospecies has not to our knowledge previously been demonstrated. Several dinoflagellate genera reportedly contain species Palbociclib in vitro with and without chloroplasts, although this may be due to unclear taxonomic boundaries based on phylogenetically unreliable characters (Larsen and Sournia 1991). As presently understood, Esoptrodinium consists of multiple rDNA phylogenetic species, but it remains unclear what morphological characters other than chloroplasts might be ultimately used to distinguish potential taxonomic species in this athecate taxon (Fawcett and Parrow 2012). Mutations observed in the psbA sequence obtained from Esoptrodinium isolate RP appear sufficient to cause loss of phototrophy. psbA encodes the D1 protein, an essential component of the photosystem II reaction center core (Bajkán et al. 2010) that is conserved in all oxygenic photosynthetic organisms (Erickson et al. 1989, Alfonso et al.
1996). The C-terminal portion of the mature D1 protein is highly conserved (Satoh 1998, Satoh and Yamamoto 2007), and the partial psbA sequence obtained in this study corresponds to this conserved region (amino acid residues 168–335 of 352 total), including transmembrane domains MCE D and E (Iida et al. 2008). The observed 26 and 21 bp deletions inferred from multiple sequence alignment of isolate RP psbA with the other Esoptrodinium and Chlamydomonas reference sequences result in the removal of 15 amino acids beginning at residue 253 of D1, followed by subsequent frame shift and nonsense mutations that would alter/eliminate 99 downstream residues of the C-terminal domain (~28% of the entire protein). A mutation at this extensive conserved region would likely cause loss of function of the D1 protein, disabling photosystem II and thus phototrophy.