The presence or absence and transcript sequences of target genes encoding for plastid-related proteins in these dinoflagellates was identified using a tBLASTn algorithm as implemented in CLC Genomic Workbench ver. 10.0.1 (QIAGEN N.V. Venlo, the Netherlands). We used a stringent E-value cutoff criterion of E-20. The amino acid sequences of the previously well-identified plastid genes were used as queries to perform tBLASTn searches (table S7). Among the plastid genes belonging to photosystem I and photosystem II, only the genes commonly identified on minicircles of dinoflagellates were analyzed in this study (Fig. 2 and table S4) (33, 34). Regarding query sequences of the psbI gene, however, identifying its orthologous genes of dinoflagellates was impossible due to its small sequence size (approximately 35 to 38 amino acids). Moreover, the possible presence of prey-originated plastid gene sequences in the transcriptome of G. smaydae was further confirmed using the strict criteria of the BLASTn algorithm (cutoff E-value <E-100 and identity >99%) against the transcriptome of the prey H. rotundata. Similarly, the identified plastid genes of the other dinoflagellates grown heterotrophically or kleptoplastically also needed to be analyzed to determine whether they are potentially evolutionarily remnant genes or just remained genes from the prey materials. However, there have been no data about the clonal strain of the prey transcriptomes, except for G. smaydae, and thus, we carried out additional homology searches for these genes against the NCBI nonredundant database. If the homology of the gene was highly similar (i.e., cutoff E-value <E-100 and identity >95%) to that of any species in the genus to which the prey species belongs, then we considered this gene as a prey-originated gene and did not include it in the heatmap. Moreover, these relationships were further validated on the basis of phylogenetic analysis (see the next section).

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