Expression of predicted Class I RNA genes. (A) Northern blot validation of different Class I RNAs from D. purpureum (DpuR), D. lacteum (DlaR), D. fasciculatum (DfaR), A. subglobosum (AsuR), and P. pallidum (DpaR). The number after the species-specific designations indicates which Class I RNA the probe recognizes. When two numbers are given, the probe recognized two different Class I RNAs. DpuR-X indicates that the probe is expected to hybridize to six different Class I RNAs predicted to be 85 nt long. DpuR-Y indicates that the probe is expected to hybridize to 24 Class I RNAs. For each organism except for D. fasciculatum (DfaR), the same membrane was probed, stripped, and reprobed for the different Class I RNAs. Radioactively labeled size marker is indicated by M, and numbers to the left indicate sizes in nucleotides. (B) Number of Class I RNA genes in each species according to the classifier. RNA-seq designate the number of expressed Class I RNA genes verified by RNA-seq. (C) ROC curves based on the RNA-seq validation and either classifier score or CM score for all Class I candidates in D. discoideum, D. lacteum, P. pallidum, and D. fasciculatum identified in the CM search. Input data are available in Supplemental Table S2. Evaluation of the classifier and CM thresholds used throughout the study are shown above the plot. Individual ROC curves for each organism are found in Supplemental Figure S3.
