Table 1.
Random PCR product, Acc. No. | Size (nt) | Initial identification | Query coverage, isolate | Query % identity, Acc. No. | Final NGS sequence identification | % identity to NGS sequence |
---|---|---|---|---|---|---|
RdRp-a MW226001 |
1,026 | ButMV | 99%a
ButMV-J |
76.27 NC_013527 |
ButMV-B | 99.81 |
RdRp-b MW226002 |
950 | GLV | 97% (DSM)b | 73.43c
KJ415259 |
HelVS-V | 99.58 |
RdRp-c MW226003 |
585 | ButMV | 99% ButMV-J |
79.79 NC_013527 | ButMV-A | 99.49 |
RdRp-d MW226004 |
439 | GLVd | 65% (DSM) | 76.21 KJ415259 |
HelVS-V | 99.54 |
CP-a MW225999 |
1,385 | ButMV | 99% ButMV-J |
79.23 NC_013527 |
ButMV-A | 99.71 |
CP-b MW226000 |
775 | ButMV | 99% ButMV-J |
81.63 NC_013527 |
ButMV-B | 99.87 |
Pairwise alignment of RdRp-a and RdRp-c revealed 74.40% identity over the full length of RdRp-c.
Deutsche Sammlung von Mikroorganismen (DSM) Gaillardia latent virus isolate 5/18-05-2010.
Separate pairwise alignment with the ButMV-J sequence AB517596 revealed only 59% coverage at 71.01% identity. Pairwise BLASTn of RdRp-b against the partial RdRp sequence of the Impatiens isolate of HelVS revealed an overlap of the 3′-terminal 177 nt of RdRp-b with the 5′ FJ555524 at 92.39% identity.
A pairwise BLASTn revealed no significant similarity to ButMV-J, but comparing RdRp-b and RdRP-d revealed a direct overlap (100% identity) of the 3′-terminal 86 nt of RdRp-d with the 5′-terminal region of RdRp-b, supporting their origin from the same source.