Figure 3

Rolling circle replicase (Rep) and capsid protein (CP) phylogenies . (A) The Rep protein phylogeny was inferred from 204 conserved amino acid positions using the Neighbor-Joining method. Bootstrap values above a 60% significance threshold, based on 1000 replicates, are shown next to the branches. NANOVIRIDAE: (SCSV) Subterranean Clover Stunt Virus, (BBTV) Banana Bunchy Top Virus. CIRCOVIRIDAE: (DfCyV) Dragonfly Cyclovirus, (BatCV) Bat Circovirus, (StCV) Starling Circovirus, (PCV2) Porcine Circovirus-2. (GOS) Global Ocean Survey paired-end read scaffolds 6801 and 10666. (B) The capsid protein (CP) phylogeny was inferred from 256 conserved amino acid positions using the Neighbor-Joining method. Bootstrap values above a 60% significance threshold, based on 1000 replicates, are shown next to the branches. TOMBUSVIRIDAE: Dianthoviruses; (RCNMV) Red Clover Necrotic Mosaic Virus, (CRSV) Carnation Ringspot Virus. Aureusviruses: (CLSV) Cucumber Leaf Spot Virus, (PLV) Pothos Latent Virus. Tombusviruses; (AMCV) Artichoke Mottled Crinkle Virus, (TBSV) Tomato Bushy Stunt Virus, (HaRV) Havel River Tombusvirus. Unclassified Tombusviridae; (PLPV) Pelargonium Line Pattern Virus. Carmoviruses; (MNSV) Melon Necrotic Spot Virus, (SgCV) Saguaro Cactus Virus, (CMtV) Carnation Mottle Virus, (TCV) Turnip Crinkle Virus. Avenavirus; (OCSV) Oat Chlorotic Stunt Virus. NODAVIRIDAE-like: (SmV-A) Sclerophthora macrospora Virus-A, (PhV-A) Plasmopara halstedii Virus-A. (GOS) Global Ocean Survey paired-end read sequence 10665. Virus proteins for which structures are available are listed with the Protein Data Bank (PDB) identification code after the virus abbreviation.