This PDF file includes:

• Legends for tables S1 to S3
• Table S4. Bacterial strains used in this study.
• Table S5. asRNAs overexpressed in M. pneumoniae.
• Legends for tables S6 and S7
• Table S8. Parameters and initial conditions used in the simulations of the asRNA effects.
• Table S9. Primers used in this study to clone the asRNAs.
• Fig. S1. Different regulatory mechanisms of sRNAs.
• Fig. S2. Theoretical and real numbers of TANAAT boxes in bacteria.
• Fig. S3. Manual annotation of sRNAs in M. hyopneumoniae.
• Fig. S4. Dependency on the AT content of different types of sRNAs.
• Fig. S5. Transcript levels of asRNAs and mRNAs in different bacteria.
• Fig. S6. Relationship between asRNAs and transcription factors in bacteria.
• Fig. S7. Simulation of the effect of the asRNAs, assuming that the pairing asRNA-mRNA causes mRNA degradation (case 2) or translation inhibition (case 3).
• References (49–67)

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Other Supplementary Material for this manuscript includes the following:

• Table S1 (Microsoft Excel format). sRNA annotation of B. aphidicola.
• Table S2 (Microsoft Excel format). sRNA annotation of M. hyopneumoniae.
• Table S3 (Microsoft Excel format). sRNA annotation of M. mycoides.
• Table S6 (Microsoft Excel format). Shotgun proteomics results of the whole proteome of the nine clones of M. pneumoniae overexpressing asRNAs.
• Table S7 (Microsoft Excel format). RNA-seq results of the whole transcriptome of the nine clones of M. pneumoniae overexpressing asRNAs.

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