Fig. 3.
Phylogenetic analysis of the four conserved closterovirus proteins and their homologues. (A) Dendrograms for the core domains of the RNA dependent RNA polymerases of closteroviruses, three animal viruses of the alphavirus-like superfamily, and SARS virus as an outgroup. Numbers indicate the number of bootstrap replicates supporting the corresponding branches; the branches with values less that 700 were collapsed. The scale bar indicates the estimated number of amino acid substitutions per site. Three genera of the family Closteroviridae are highlighted with the color-coded ellipsoids. GLRaV-2, Grapevine leafroll-associated virus-2 (Zhu et al., 1998); CYSDV, Cucurbit yellow stunting disorder virus (Aguilar et al., 2003); GLRaV-1, Grapevine leafroll-associated virus-1 (Fazeli and Rezaian, 2000); PMWaV-2, Pineapple mealybug wilt-associated virus-2 (Melzer et al., 2001); other designations are as in Fig. 2. (B) Dendrograms for the papain-like proteinase domains of the closterovirus leader proteinases. CTV and GLRaV-2 each possess two leader proteinases, L1 and L2. EAV-nsp1, the nonstructural protein-1, a papain-like leader proteinase of Equine arteritis virus used as outgroup. (C) Dendrograms for the Hsp70 homologues from the closteroviruses, the mimivirus, prokaryotes, and eukaryotes. (D) Dendrograms for the CP-like domains present in closterovirus CPs, CPms, and p60s. GLRaV-1 encodes two divergent variants of CPm, 1 and 2. PVA-CP, capsid protein of Potato virus A, an outgroup.
Sequences alignment and phylogenetic analysis were performed using the Clustal X 1.8 program (Thompson et al., 1997) and MEGA 3.1 (Kumar et al., 2004). Trees were generated using the Neighbour-Joining method (Saitou and Nei, 1987) with correction for multiple substitutions and 1000 bootstrap replicates. In all cases, similar trees and bootstrap values were obtained using the maximum parsimony method (Fitch, 1977) (not shown). The NCBI accession numbers for closteroviruses were as follows. GLRaV-3, NC004667; PMWaV-2, AF283103; GLRaV-1, AF195822; BYV, NC001598; CTV, NC001661; GLRaV-2, NC007448; LIYV, NC003617 and NC003618; SPCSV, NC004123 and NC004124; CYSDV, NC004810 and NC004809. The additional viral sequences used were NP056786 of Hepatitis E virus, NC001545 of Rubella virus RdRp, NC001547 of Alphavirus, NC004718 of SARS virus, NP705583 of Equine arteritis virus, NP734368 of Potato virus A. The Hsp70 sequences were: XP470141, XP475261, AAO17017 for O. sativa; CAA05547, NP198206, NP199802, CAB89371 for A. thaliana; NP646617 for D. discoideum; NP002146, P11021, P38646 for H. sapiens; YP 142608, AAV50662 for A. polyphaga mimivirus; NP492485 for C. elegans; Q8YW74 for Nostoc spp.; NP414555 for E. coli; NP454622 for S. enterica; NP794258 for P. syringae; XP762364 for U. maydis.