C. elegans genes showing correlated conservation patterns with RDE-1 are predicted to function in small RNA pathways such as miRNA and siRNA-based gene silencing. The signature phylogenetic profile of the Argonaute proteins is that they are absent in 9 out of 31 Ascomycota species, 1 out of 3 Basidiomycota species, and 6 out of 14 protist species, but have not been lost in any of the 33 animal or 6 land plant species compared. High-confidence candidates from this analysis were tested for defects in RNAi silencing. RDE-1 was used to generate a rank-order list of proteins with the similar phylogenetic profiles.
Validated miRNA and siRNA pathway proteins with a shared phylogenetic profile. The driving pattern of this phylogenetic profile correlation is strong conservation in all animals and particular protists, but no homologue in any of the fungi or plants tested. DCR-1 was used to generate a rank-order list of proteins with the similar phylogenetic profiles.