The origins of apicomplexan sequence innovation

BLAST searches were performed to identify sequence similarity between apicomplexan sequences from both partial and complete genomes. See Supplemental Table S5 for the BLAST programs used. All of the species identified to match an apicomplexan sequence were placed in one of the following eight taxonomic groups: (ap) Apicomplexa; (al) other Alveolata; (op) other protists; (fu) Fungi; (me) Metazoa; (vi) Viridiplantae; (ba) Bacteria; and (ar) Archaea. This allowed the creation of a binary profile for each protein detailing presence (“1”) or absence (“0”) in a specific taxon. The results at three-bit score cutoffs are presented. In the bottom four profiles, the binary state of at least one taxon has been turned into a wild card, permitting the grouping of specific profiles. For example, profile “..0001..” indicates sequences that match a plant species but have no match in other Protists, Fungi, and Metazoa.