Extended Data Fig. 3: Updated classification of CRISPR types II and VI.
From: An updated evolutionary classification of CRISPR–Cas systems including rare variants
a,b, The figure schematically shows representative (typical) CRISPR–cas loci of each type II (a) and type VI subtype (b) and selected distinct variants, with the dendrogram on the left showing the likely evolutionary relationships between the types and subtypes. The column on the right indicates the organism and the corresponding gene range. Homologous genes are colour-coded and identified by a family name following the previous classification8. Where both a systematic name and a legacy name are commonly used, the legacy name is given under the systematic name. The grey shading of different hues shows the two levels of classification, subtypes and variants. The adaptation module genes cas1 and cas2 are present in only a subset of the subtype VI-A and VI-D loci and are accordingly shown by dashed lines. The WYL-domain-encoding genes and csx27 genes are also dispensable and thus shown by dashed lines. Additional genes encoding components of the interference module, such as tracrRNA, are shown. The domains of the effector proteins are colour-coded: RuvC-like nuclease, green; HNH nuclease, yellow; HEPN RNase, purple; transmembrane domains, blue. DNA and RNA are the molecules targeted by the systems. c, Deep relationships among type VI effector families. Profile–profile comparisons were performed and the UPGMA dendrogram was constructed as described in Methods. The tree is based on the most conserved C-terminal HEPN domain alignments only. HHsearch was run with the minimum length coverage for hits set to l = 0.33, -u = 2.3 -gcut = 0.667. Multiple alignments (profiles) of the C-terminal HEPN domains are available in data file 5 in ref. 15, and the original tree is available in data file 4 in ref. 15. The dashed line corresponds to the tree depth D between 1.5 and 2 (D = 2 roughly corresponds to the pairwise HHsearch similarity score of exp(2D) ≈ 0.02 relative to the self-score) and separates most of the subtypes assigned previously or in this work. New subtypes are highlighted by blue. d, Organization of representative loci for distinct variants of subtype VI-B. Designations are the same as in b.
