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. 2014 Sep 30;9(9):e108653. doi: 10.1371/journal.pone.0108653

Figure 3. Sequence relationships of C. parasitica RDR-like proteins with putative and known RDRs in other eukaryotes.

Figure 3

RdRP domains were extracted from each sequence and aligned for tree reconstruction as described in the Methods. The four RDR-like C. parasitica sequences are shown in shaded boxes; two alternatively spliced forms of RDR4, identified by cDNA sequencing (resulting in a truncated RdRP domain) are shown. The RDRs in N. crassa are indicated by asterisks and were used to name the three fungal RDR clades, indicated on the right, along with the clades containing RDR sequences in other eukaryotes. Sequence accessions and species names are the following: An1 = AN2717 (Aspergillus nidulans); An2 = AN4790 (A. nidulans); AtRdRP1 = NP_172932.1, RNA-dependent RNA polymerase 1 (Arabidopsis thaliana); AtRdRP3 = NP_179581.2, RNA-dependent RNA polymerase-like protein (A. thaliana); BfRDR1 = AAQ10792.1, RNA-directed RNA polymerase-like protein (Branchiostoma floridae); CeEGO-1 = NP_492132.1, Protein EGO-1 (Caenorhabditis elegans); CnRdRP = ACJ04634.1, RNA-dependent RNA polymerase (Cryptococcus neoformans var. grubii); Cprdr1 = HF912382, putative RNA-dependent RNA polymerase (Cryphonectria parasitica); Cprdr2 = HF912383, putative RNA-dependent RNA polymerase (C. parasitica); Cprdr3 = HF912384, putative RNA-dependent RNA polymerase (C. parasitica); Cprdr4 = HF912385, putative rdr4 pseudogene (C. parasitica); DdDosA = AF117611_1, DosA protein (Dictyostelium discoideum); DdRdRP = EAL62541.1, RNA-directed RNA polymerase (D. discoideum); Mcrdrp-1 = JGI scaffold_05∶2640291–2644233 (Mucor circinelloides); Mcrdrp-2 = JGI scaffold_05∶245898–249911 (M. circinelloides); Mo1 = EHA51817.1, RNA-dependent RNA polymerase (Magnaporthe oryzae); Mo2 = EHA52286.1, RNA-dependent RNA polymerase (M. oryzae); Mo3 = EHA46264.1, RNA-dependent RNA polymerase 1 (M. oryzae); MtRdRP = XP_003608944.1, RNA-dependent RNA polymerase (Medicago truncatula); NcQDE-1 = AJ133528, qde-1 gene (Neurospora crassa); NcRRP-3 = XP_963405, hypothetical protein (N. crassa); NcSAD1 = AAK31733, suppressor of ascus dominance (N. crassa); Os701 = NP_918046.1, putative RNA-directed RNA polymerase (Oryza sativa); Os702 = NP_913147.1 (O. sativa); PtRDRP1 = CAI39057.1, RNA-dependent RNA polymerase (Paramecium tetraurelia); SpRdp1 = CAB11093.1, RNA-directed RNA polymerase Rdp1 (Schizosaccharomyces pombe); SlRdRP = CAA71421.1, RNA-directed RNA polymerase (Solanum lycopersicum).