Predicted aa sequences of each gene were aligned with homologs from related organisms using CLUSTAL W (1.8) and inspected manually. Phylogenetic relationships of P. marinus with alveolate relatives and other eukaryotes were inferred using Neighbor Joining (NJ), Maximum Likelihood (ML), and MrBayes (MB) analyses. NJ analysis was performed online [http://clustalw. ddbj.nig.ac.jp/top-e.html] with the default setting. For ML tree reconstruction, the datasets were run through ProtTest [25] to identify the best-fitting aa substitution models (Table 3) , which were then employed in the phylogenetic analysis using PhymLv3.0 [26] . MB analysis was carried out with 20,000-1,000,000 MCMC generations depending on when the average standard deviation of split frequencies reached below 0.01, a tree sampling frequency of 10-100, and 25% of generations discarded as burn-in [27] . To verify the reliability of the tree topologies, branch support was estimated based on bootstrap (1,000 resamplings) in NJ, approximate Likelihood Ratio Test (aLRT) in ML, and posterior probability in MB.