Ribosomal proteins (RPs) from dinoflagellates [21] were used to query the P. marinus genome and GenBank databases to retrieve RPs from P. marinus, apicomplexans, ciliates, diatoms and other eukaryotic representatives. Since many of the dinoflagellate RP cDNAs available were not full-length, to maximize phylogenetic information from these genes, 22 full-length cDNAs of RPs from dinoflagellates Amphidinium carterae CCMP1314 and K. veneficum CCMP2778 were cloned using dinoflagellate-specific SL coupled with 39 RACE as described previously ( [8] ; GenBank accession # GU372975-GU373034). To diversify the gene markers for phylogenetic analyses, another 12 conserved gene sequences were collected from our ongoing cDNA sequencing project for these two species, and their 59 and 39 ends achieved using RACE as necessary. Using these as queries, homologs were collected from GenBank for P. marinus and other species mentioned above. The absence of histones, long considered a benchmark of typical dinoflagellates, is erroneous (see [21] for review); thus, histone genes were retrieved from the Perkinsus genome project database. Full-length or nearly full-length mt cox1 and cob sequences were also obtained from P. marinus and P. chesapeaki. The 39 end of cob for both Perkinsus spp. was obtained using the 39 RACE technique with Perkinsus cob primers paired with GeneRacer3 primer (Invitrogen). All of these genes were used in phylogenetic analyses.