Extended Data Fig. 10: Co-occurrence of pAgo proteins, DSB repair systems and CRISPR–Cas in prokaryotic genomes.
From: DNA targeting and interference by a bacterial Argonaute nuclease
a, Circular phylogenetic tree of pAgos from prokaryotic strains with fully assembled genomes based on the multiple alignment of the MID-PIWI domains. Three major phylogenetic groups of pAgos are indicated4: long-A pAgos usually contain all characteristic domains of the Ago family (N, PAZ, MID and PIWI) and have a predicted nuclease site; long-B pAgos also contain all domains but are inactive; and short pAgos contain only MID and PIWI domains and are inactive. The pAgo proteins were annotated as follows, from the inner to the outer circles: the superkingdom to which the corresponding pAgo belongs; the type of the PIWI domain, depending on the presence of the catalytic tetrad DEDX; the type of the DSB repair system encoded in the corresponding genome; the class of CRISPR–Cas system; the type and subtype of CRISPR–Cas system. CbAgo, T. thermophilus Ago (TtAgo) and Marinitoga piezophila Ago (MpAgo) are highlighted in red. The scale bar represents the evolutionary rate calculated under the JTT+CAT evolutionary model. b, The distribution of various subtypes of type I and type III CRISPR–Cas system in the fully assembled genomes encoding pAgos. The number of genomes for each pAgo group is indicated.
