PmaSLRNAs are distinct from dinoflagellate SL RNAs. In the apparent Sm-binding site, instead of a ''TTTT'' motif conserved in dinoflagellates, PmaSL has ''TCTT'' or ''TCT''. The intron region of the SL RNA in dinoflagellates is conserved, but the similarities diminish in Amoebophrya, a parasitic lineage currently considered to represent the most ancient dinoflagellate [30] . SL RNAs in P. marinus display similar divergence from dinoflagellates, with a substantially longer intron relative to the core dinoflagellates and Amoebophrya, suggestive of an earlier divergence for P. marinus. The SL RNAs in other SL trans-splicing eukaryotes range from 46 nt in the urochordate Ciona intestinalis to 142 nt in Trypanosoma brucei. The SL RNA transcripts in P. marinus range from 80-83 nt, and are ,83 nt in P. chesapeaki. Thus, Perkinsus SL RNAs have unique features in comparison to dinoflagellates, and Perkinsus spp. may represent the earliest trans-splicing lineage within Alveolata, separated from the non-trans-splicing Ciliophora and Apicomplexa [8] , yet distinct from the Dinoflagellata. Given the high diversity of the parasitic Syndiniales class of dinoflagellates [31] , the uncharacterized marine alveolate group I that lies between Perkinsus and the core dinoflagellates ( [7] and references therein) should be examined for the presence of additional types of SL RNA.