Genome-wide analysis of small RNA biogenesis proteins refine the evolution of Dicer-like and Argonaute gene families in flowering plants

Several protein families play a role in the biogenesis and function of small RNAs (sRNAs) in plants. Among these are Dicer-like (DCL), RNA-directed RNA polymerase (RDR), and Argonaute (AGO) proteins, as well as accessory proteins such as double-stranded RNA-binding (DRB), SERRATE (SE), and SUPPRESSION OF SILENCING 3 (SGS3) that are co-factors of DCL and RDR proteins. Here, we present phylogenetic analyses of seven sRNA pathway protein families performed on 198 species in the Viridiplantae. We show that the eudicot DCL3 protein is orthologous to the monocot DCL5, indicating that the monocot DCL3 has diverged and specialized in heterochromatic siRNA production. We found 167 highly conserved amino acids conserved among monocot DCL3/DCL4/DCL5 sequences. Amino acids conserved between DCL3 and DCL5 were located in the Helicase and RNase domains while amino acids conserved between DCL4 and DCL5 were mostly in the dsRNA binding and PAZ domains. Absent in DCL4, we found protein regions common to DCL3/DCL5 near both extremities of the PAZ domain which can potentially increase the distance from the RNase III catalytic center and thus determine the product size. We identified multiple duplication events of AGOs that had been lost, retained or further duplicated in sub-groups, indicating that the evolution of AGOs is complex in monocots, suggesting that functional studies in model species might not be easily translated to other species. This work provides an evolutionarily coherent and standardized annotation for gene families involved in plant sRNA biogenesis. ### Competing Interest Statement The authors have declared no competing interest.