Phylogenetic tree for the Argonaute family of proteins. A phylogenetic tree based on Argonautes (AGOs) from a variety of species, with major clades indicated based on Arabidopsis AGO proteins. Two AGO proteins (AGO716 and AGO710) were removed from the trees because of long branches. The code for each AGO protein is based on the ChromDB identifier plus the species from which the AGO was derived, with plant proteins using the following system of codes: ARATH, Arabidopsis thaliana; POPTR, Populus trichocarpa; ORYSA, Oryza sativa ssp. japonica (from the Nipponbare sequence); ORYSAI, Oryza sativa ssp. indica (from the 93–11 sequence). The phylogenetic methods are described in the legend for Supplementary Fig. 1.