Fig. 1

Clustered Interspaced Short Palindromic Repeats (CRISPR)-Cas Subtype I-B in Candidatus M. intestinalis and its targets in smacoviruses. The CRISPR-Cas subtype I-B in Ca. M. intestinalis is represented. Related cas genes are grouped and coloured according to functional categories: adaptation (cas1–2 and cas4), target cleavage (cas3) and formation of interference complex (cas6, cas8a1, cas7 and cas5). Cas8a1 would belong to subtype I-A. Two repetitive arrays are found in opposite orientations, here named B1 (112 repeats) and B2 (3 repeats), with putative leader sequences, from where transcription would start. Array B1 is amplified and similarities of spacers to sequences in smacoviruses indicated. A smacovirus 'archetype' is depicted where targets are represented with their relative positions to genes (see Methods). Similar sequences that are in the same orientation of spacers point right and vice versa. Smacoviruses are circular single-stranded DNA (ssDNA) virus with just two genes (rep and cap). Targets in the ssDNA are represented below the viral genome, and targets in the complementary strand above. Targets in red were found with local–global alignments, while targets in grey only with local alignments. All arrows point in the sense of predicted transcription (for targets transcription of CRISPR RNA (crRNA)). Scale bars are 5 kb (above) and 0.5 kb (bottom). Non-CRISPR genes are coloured violet