Phylogenetic and protein domain analysis of Dicer proteins. (a, b) Phylogenetic analysis of Dicer proteins (a) and with Drosha as an outgroup (b). The tree in (a) was composed based on the alignments of full-length Dicer proteins without dsRBD (c, red underline), while the tree in (b) was based on the RNase I domain (c, blue underline). The Drosophila and Tribolium Dcr-1 proteins cluster together, indicating clear orthology. In contrast, orthology of Dcr-2 proteins in these insects is less clear since they do not cluster together. (c) Domain architecture of Dicer proteins. Although our phylogenetic analysis cannot solve the orthology of insect Dcr-2 proteins, the similarity in the domain architectures of Dm-Dcr-2 and Tc-Dcr-2 suggests that they might be orthologous. Tc-Dcr-1 has a similar domain architecture to Ce-Dcr-1, which is involved both in RNAi and miRNA pathways, suggesting that Tc-Dcr-1 might also be involved in both pathways (unlike Dm-Dcr-1, which is involved only in the RNAi pathway). The ScanProsite scores are shown and the location of domain truncations is indicated. The first helicase domain in Dm-Dcr-1 and dsRBD in Tc-Dcr-2 (indicated by an asterisk) are not recognized by ScanProsite but some conserved residues are identified by ClustalW alignment.