Next generation sequencing is quickly emerging as the go-to tool for plant virologists when sequencing whole virus genomes, and undertaking plant metagenomic studies for new virus discoveries. This study aims to compare the genomic and biological properties of Bean yellow mosaic virus (BYMV) (genus Potyvirus), isolates from Lupinus angustifolius plants with black pod syndrome (BPS), systemic necrosis or non-necrotic symptoms, and from two other plant species. When one Clover yellow vein virus (ClYVV) (genus Potyvirus) and 22 BYMV isolates were sequenced on the Illumina HiSeq2000, one new ClYVV and 23 new BYMV sequences were obtained. When the 23 new BYMV genomes were compared with 17 other BYMV genomes available on Genbank, phylogenetic analysis provided strong support for existence of nine phylogenetic groupings. Biological studies involving seven isolates of BYMV and one of ClYVV gave no symptoms or reactions that could be used to distinguish BYMV isolates from L. angustifolius plants with black pod syndrome from other isolates. Here, we propose that the current system of nomenclature based on biological properties be replaced by numbered groups (I–IX). This is because use of whole genomes revealed that the previous phylogenetic grouping system based on partial sequences of virus genomes and original isolation hosts was unsustainable. This study also demonstrated that, where next generation sequencing is used to obtain complete plant virus genomes, consideration needs to be given to issues regarding sample preparation, adequate levels of coverage across a genome and methods of assembly. It also provided important lessons that will be helpful to other plant virologists using next generation sequencing in the future.

Wheat streak mosaic virus (WSMV) infection and infestation with its wheat curl mite (WCM; Aceria tosichella) vector were investigated in wheat crops at two sites in the low-rainfall zone of the central grainbelt of south-west Australia. In the 2006 outbreak, after a preceding wet summer and autumn, high WCM populations and total infection with WSMV throughout a wheat crop were associated with presence of abundant grasses and self-sown ‘volunteer’ wheat plants before sowing the field that became affected. Wind strength and direction had a major effect on WSMV spread by WCM to neighbouring wheat crops, the virus being carried much further downwind than upwind by westerly frontal winds. Following a dry summer and autumn in 2007, together with control of grasses and volunteer cereals before sowing and use of a different seed stock, no WSMV or WCM were found in the following wheat crop within the previously affected area or elsewhere on the same farm. In the 2007 outbreak, where the preceding summer and autumn were wet, a 40% WSMV incidence and WCM numbers that reached 4800 mites/ear at the margin of the wheat crop were associated with abundant grasses and volunteer wheat plants in adjacent pasture. WSMV incidence and WCM populations declined rapidly with increasing distance from the affected pasture. Also, wheat plants that germinated early had higher WSMV infection incidences than those that germinated later. The alternative WSMV hosts identified at these sites were volunteer wheat, annual ryegrass (Lolium rigidum), barley grass (Hordeum sp.), and wild oats (Avena fatua). In surveys outside the growing season at or near these two sites or elsewhere in the grainbelt, small burr grass (Tragus australianus), stink grass (Eragrostis cilianensis), and witch grass (Panicum capillare) were identified as additional alternative hosts.

Losses in seed yield and quality caused by infection with Beet western yellows virus (BWYV) alone or in combination with direct feeding damage by Myzus persicae (green peach aphid) were quantified in field experiments with Brassica napus (canola, oilseed rape) in the ‘grainbelt’ region of south-western Australia. Plants infected with BWYV and infested with M. persicae were introduced into plots early to provide infection sources and spread BWYV to B. napus plants. Insecticides were applied as seed dressings and/or foliar applications to generate a wide range of BWYV incidences in plots. Colonisation by vector aphids and spread of BWYV infection were recorded in the plots of the different treatments. At sites A (Medina) and B (Badgingarra) in 2001, foliar insecticide applications were applied differentially at first, but, later, ‘blanket’ insecticide sprays were applied to all plots to exclude any direct feeding damage by aphids. When BWYV infection at sites A and B reached 96% and 100% of plants, it decreased seed yield by up to 46% and 37%, respectively. Also, variation in BWYV incidence explained 95% (site A) and 96% (site B) of the variation in yield gaps, where for each 1% increase in virus incidence there was a yield decrease of 12 (site A) and 6 (site B) kg/ha. At both sites, this yield decline was entirely because fewer seeds formed on infected plants. At site B, BWYV infection significantly diminished oil content of seeds (up to 3%), but significantly increased individual seed weight (up to 11%) and erucic acid content (up to 44%); significant increases in seed protein content (up to 6–11%) were recorded at both sites. In field experiments at sites B and C (Avondale) in 2002, insecticides were applied as seed dressings or foliar sprays. At site B, when BWYV incidence reached 98%, the overall yield loss caused by BWYV and direct M. persicae feeding damage combined was 50%. At site C, when BWYV incidence reached 97%, the overall combined yield decline caused by BWYV and direct feeding damage was 46%. This research under Australian conditions shows that, when aphids spread it to B. napus plantings such that many plants become infected at an early growth stage, BWYV has substantial yield-limiting potential in B. napus crops. Although the results represent a worst case scenario, the losses were greater than those reported previously in Europe and are cause for concern for the Australian B. napus industry. When applied at 525 g a.i./100 kg of seed, imidacloprid seed dressing controlled insecticide-resistant M. persicae and effectively suppressed spread of BWYV for 2.5 months and increased seed yield by 84% at site B and 88% at site C. Therefore, provided that mixing the insecticide with seed is sufficiently thorough, dressing seed with imidacloprid before sowing provides good prospects for control of BWYV and M. persicae in B. napus crops.

The ever increasing movement of viruses around the world poses a major threat to plants growing in cultivated and natural ecosystems. Both generalist and specialist viruses move via trade in plants and plant products. Their potential to damage cultivated plants is well understood, but little attention has been given to the threat such viruses pose to plant biodiversity. To address this, we studied their impact, and that of indigenous viruses, on native plants from a global biodiversity hot spot in an isolated region where agriculture is very recent (<185 years), making it possible to distinguish between introduced and indigenous viruses readily. To establish their potential to cause severe or mild systemic symptoms in different native plant species, we used introduced generalist and specialist viruses, and indigenous viruses, to inoculate plants of 15 native species belonging to eight families. We also measured resulting losses in biomass and reproductive ability for some host–virus combinations. In addition, we sampled native plants growing over a wide area to increase knowledge of natural infection with introduced viruses. The results suggest that generalist introduced viruses and indigenous viruses from other hosts pose a greater potential threat than introduced specialist viruses to populations of native plants encountered for the first time. Some introduced generalist viruses infected plants in more families than others and so pose a greater potential threat to biodiversity. The indigenous viruses tested were often surprisingly virulent when they infected native plant species they were not adapted to. These results are relevant to managing virus disease in new encounter scenarios at the agro-ecological interface between managed and natural vegetation, and within other disturbed natural vegetation situations. They are also relevant for establishing conservation policies for endangered plant species and avoiding spread of damaging viruses to undisturbed natural vegetation beyond the agro-ecological interface.