Fig. 2

Complete apicoplast annotation and identification of core apicoplast proteins. a Draft annotations from C. cayetanensis reference genome (Cc-Ref) were aligned with KP866208 (Cc-HEN01 C. cayetanensis HEN01 strain), AY217738 (E.tenel: Eimeria tenella). The annotations were then manually curated to define gene boundaries (Table 1) and to correct any anomalies (b and c) in the assemblies. The final C. cayetanensis reference genome annotations were compared with LN999985 (P.falci: Plasmodium falciparum 3D7) and predicted proteins from other apicomplexan apicoplasts available in GenBank Twenty-nine core proteins present in most of the available apicoplast genomes were identified in the C. cayetanensis reference Table 1. Core apicoplast proteins 1–29 in C. cayetanensis (track Cc-ref) are illustrated above from left to right. In Tracks a-c, arrows in rRNA CDS are in red, tRNA in purple and proteins are in blue. In Track d, only the predicted proteome is shown in dark blue. b Cyclospora homolog of RPL36 (ribosomal protein L36) was included (track Cc-Ref) between RPS5 and RPS11 in the reference genome annotation. This partial peptide homologous to an Eimeria protein (track E.tenel) is not available (indicated by a red line) from the KP866208 genome annotation file in GenBank (track Cc-HEN01). c Based on the core apicoplast proteins identified in a wide variety of apicomplexan parasites, a homolog of ORF-A protein found in C. cayetanensis reference genome (track Cc-Ref) was predicted and confirmed to be present in Eimeria (track E.tenel). Currently this CDS is missing (indicated by a red line) from the annotations of E. tenella (AY217738) and other eimeriids. Track Cc-HEN01 represents the apicoplast coding regions of strain C. cayetanensis HEN01