Table 1.
OMMV and TNV-D isolates present in single and in double infected plant samples and Genbank sequences used in coat protein variability analysis.
Figure 1.
Nucleotide and deduced amino acid diversities along the OMMV and TNV-D CP gene.
Left - OMMV and TNV-D aa and nt CP sequences; Right top – OMMV aa and nt CP sequences; Right bottom – TNV-D aa and nt CP sequences. Nucleotide diversity values were obtained in successive windows of 81 nt and amino acid diversity was obtained in successive windows of 26 aa.
Figure 2.
Phylogenetic tree analysis of OMMV and TNV-D isolates based on CP nt sequences.
NJ tree was constructed from the sequence alignment of ca. 870 nts of OMMV and TNV-D CP coding region from 65 clones of OMMV and 55 TNV-D isolates and from 11 sequences retrieved from the GenBank database, totalling 131 sequences. Repeated sequences within each isolate were omitted. Each sequence variant was named with a letter (A, B, C,…) following the isolate designation to allow differentiation. Phylogenetic analysis included 78 sequences. Multiple sequence alignments were generated using MEGA 5.1, and phylogenetic tree was constructed by the NJ algorithm, based on calculations from pairwise nt sequence distances for gene nt analysis. Bootstrap analysis was done with 1000 replicates. Numbers above the lines indicate bootstrap scores out of 1000 replicates.
Figure 3.
Multiple sequence alignment of the deduced amino acid sequences of OMMV variants analysed: WT (OMMV_GP, reference sequence, NC_006939.1), Q20L, Q32R, I133V and A216T.
Figure 4.
Multiple sequence alignment of the deduced amino acid sequences of TNV-D variants analysed: WT (TNV-DH, NC_003487.1), G5R, F13I, S17T, A23N, S129P, N227D, C230R, A244S, E261K.
Figure 5.
Three-dimensional representation of the OMMV (left) and TNV-D (right) coat protein, highlighting mutations.
Mutations are rendered in spheres. Each trimmer is coloured in light green, magenta and cyan. A – Virus minimum contact unit; B – The surface exterior; C – The surface interior.