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International Advances in Plant Virology in conjunction with Cost Action FA1407, Greenwich, UK 7th – 9th September 2016
The Association of Applied Biologists organised a joint meeting with COST Action FA1407 (Application of next generation sequencing for the study and diagnosis of plant viral diseases in agriculture) in September 2016. The conference was held on the grounds of the Old Royal Naval College in Greenwich, UK and was very well attended with more than a 100 participants from all over the world. A major focal point was next generation sequencing and its application in plant virology.
Numerous presentations covered a wide range of NGS applications as well as methodological questions. Hano Maree used NGS for virus detection and compared different extraction methods for nucleic acids. Depending on whether one wants to assemble whole genomes of a virus or detect novel viruses by de novo assembly, different extraction methods such as ribo-depleted RNA or sRNAs were suggested. However, depending on the sequencing depth, sRNAs sequencing may not be the best option for all viruses as e.g. Citrus tristeza virus required a high sequencing depth for full genome recovery using the sRNA approach. Other presenters reported on the use of NGS for virus discovery in crops (barley, vegetables, grapevine) and other matrices such as waste water as well as for transcriptome studies or certification schemes. A report on a bioinformatic proficiency testing demonstrated the importance of bioinformatics in the analysis of NGS data. Although being supplied with the same raw data set, each of the participating laboratories used their own bioinformatic pipeline. Even if the same software packages were used, slight differences in the settings lead to variable results: not everyone was able to discover all viruses from the given data sets; some (low titre) viruses were missed repeatedly by several labs. Although the false positive discovery rate was low, it was concluded that it was difficult to suggest one standard pipeline; perhaps several work-flows were needed to be combined for reliable virus detection.
Another section dealt with molecular biology of virus resistance and the latest developments in this field. Although, for example, the recessive resistance genes in lettuce against Lettuce mosaic virus (LMV) have been known for a long time, the knowledge of the molecular interactions is still patchy. The recessive resistance genes encode for an eukaryotic translation initiation factor, a susceptibility factor for LMV. However, this resistance can be overcome by the virus, the VPg was known to be the resistance- breaking determinant. Sylvie German-Retana reported that also the cylindrical inclusion helicase was able to overcome LMV resistance, non-lettuce isolates of LMV could adapt to LMV resistance in lettuce by acquiring mutations in the cylindrical inclusion helicase.
Plant viruses are not always “bad guys” causing diseases but are also increasingly used for nanobiotechnogy. George Lomonossoff and Christina Wege reported how plant viruses could be used in nantotechnology to produce e.g. artificial virus-like particles with defined amino acid changes on the surface of these particles. It is possible to use these nanoparticles as carriers for enzymes with potential application in diagnostics or as electrochemical biosensors.
Of personal interest was the session on virus-vector interactions. During my PhD we discovered that plant viruses can manipulate their hosts to influence their vectors. Currently, more and more interactions between viruses, their hosts and their vectors are discovered.
One of the latest findings was reported by Sanjie Jiang from John Carr’s lab: bumble bees were allowed to pollinate flowers of mock- or Cucumber mosaic virus (CMV)-infected tomatoes. Surprisingly, CMV-infected tomatoes showed a higher pollination rate as seen in increased seed yield. This “bee pollination service” might be beneficial for both the virus and the plants: increased reproduction of CMV susceptible tomatoes will ensure suitable host plants for the virus under natural conditions and increased pollination will allow enhanced reproduction of the plants.
There were many more excellent talks on all aspects of virology ranging from the discovery of novel viruses (we reported on accidentally finding a novel virus in New Zealand) over populations dynamics to virus-host interactions and virus-vector interactions. Unfortunately, this report does not allow more details.
Two more presentations should be acknowledged nevertheless: Roger Hull presented the past and present of plant virology and speculated about the future developments in plant virology.
Well-known as the author of several important standard text books, Roger addressed many open questions that have not been resolved yet despite many advances in plant virology (“What is the origin of viruses?”, “Are there fern viruses? Moss viruses?”). A huge credit needs to be given to Prof. Andrew Westby (Natural Resources Institute) who held a memorial lecture to honour Michael (Mike) Thresh. Mike passed away in 2015 and was posthumous honoured at the International Plant Virus Epidemiology Symposium in 2016 as “Father of Plant Virus Epidemiology”.
He was internationally well known and worked on many different cropvirus combinations during his career.
More details on Mike’s live and work can be found at the obituaries on the ICPVE or National Ressources Institute websites (http://www. isppweb. org/icpve/ and http://www. nri. org/news/2015/ remembering-professor-mike-threshinspirational- hands-on-plant-virologist).
I am very grateful for the financial support of the BSPP that enabled me to participate at this excellent meeting!
Dr. Heiko Ziebell Julius Kühn-Institut, Germany