Mutation rate in Velvet tobacco mottle virus varies between genomic region and virus variant but is not influenced by obligatory mirid transmission K. Arthur • N. C. Collins • J. W. Randles Received: 12 June 2012 / Accepted: 27 July 2012 Ó Springer Science+Business Media, LLC 2012 Abstract Genomic mutation in plant viruses of cultivated plants is known to be influenced by virus, host and vector, but the factors influencing mutation in viruses of native plants in natural ecosystems are rarely studied. We have tested the effect of mode of transmission on mutation in Velvet tobacco mottle virus (VTMoV), a mirid-vectored sobemovirus associated with Nicotiana velutina, an Aus- tralian native xerophyte growing in a region isolated from anthropogenic influences. Two variants of VTMoV (K1 and R17) were passaged monthly in the alternative exper- imental plant host, N. clevelandii, for 2 years, either by mechanical inoculation or by transmission with the mirid Cyrtopeltis nicotianae. Sequence variations were scored after 24 passages in regions of the genome containing the open reading frames (ORFs) for the P1 and coat protein (CP). The mean mutation rate was 6.83 9 10 -4 nt/site - year, but a higher overall rate was observed for the K1 (satellite -) than the R17 (satellite ?) variant. The P1 ORF showed a higher frequency of non-synonymous mutations than the CP. No clear association was found between either mutation site or mutation rate and the mode of transmis- sion, indicating that obligatory mirid transmission had not exerted a specific bottle-neck effect on sequence variation during the experimental time frame. Failure to detect any sequence motifs linked to vector transmission suggests that a specific capsid-stylet interaction is not required for transmission by mirids. Keywords Cyrtopeltis nicotianae  Mirid transmission  Native plant virus  Sobemovirus  Velvet tobacco mottle virus  Virus mutation rate Introduction RNA mutation rates in plant viruses are influenced by host species [1, 2], vectors [3–5] and locations in the host [6, 7] and can also differ between genomic regions [1]. Previous studies have focused primarily on viruses causing diseases of cultivated plants, while mutation rates of viruses of native non-cultivated plants are rarely available for com- parison. Velvet tobacco mottle virus (VTMoV); genus Sobemovirus [8], is a positive-sense, single-stranded RNA virus with a genome comprising 4,247 nt. VTMoV is a naturally occurring mirid-transmitted virus of Nicotiana velutina, a species of the arid ecosystem of north-eastern South Australia. Using its native vector, Cyrtopeltis (syn. Engytatus) nicotianae (Koningsberger)(Miridae) in com- bination with the experimental host, N. clevelandii, VTMoV has been shown to have an unusual long term but intermittent mode of transmission which has characteristics of both non-persistent and persistent non-circulative transmission [8, 9]. The mechanism of this non-persistent transmission has not been studied, but the explanation proposed for persistent transmission is that the virus is ingested and accumulates in the gut, where it retains infectivity for up to 9 days [10]. It could then either be K. Arthur  J. W. Randles School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia Present Address: K. Arthur (&) The New Zealand Institute for Plant & Food Research Ltd, Private Bag 92169, Auckland 1142, New Zealand e-mail: kieren.arthur@plantandfood.co.nz N. C. Collins Australian Centre for Plant Functional Genomics (ACPFG), School of Agriculture, Food and Wine, University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia 123 Virus Genes DOI 10.1007/s11262-012-0801-2