Posted on behalf of Andrew Taylor, PhD candidate Murdoch University and Research Officer DPIRD WA (andrew.taylor@dpird.wa.gov.au)
By 2028 genome sequencing will be common place amongst laboratories as technology improves and costs fall. This will result in more organisms having their genome sequenced and will lead to the taxonomic re-evaluation of a number of economically important plant pathogens. The oomycetes are one group of plant pathogens that are economically important to a diverse number of horticultural commodities and amongst natural ecosystems. In many instances they are also known to develop fungicide resistance rapidly, making control problematic. It appears from the number of oomycetes that have had their genome sequenced a taxonomic re-evaluation is likely.
A characteristic of a number of oomycetes is that they are obligate biotrophs, meaning they can only be stored in culture collections on samples of the infected host. Often only a few of these representative samples exist and the collection dates are sporadic, in many cases multiple decades apart. This creates issues for researchers as it means samples lodged in collections are not allowed to be released as DNA extractions are considered destructive sampling. It also creates issues with biosecurity policy. With the likely taxonomic changes as a result of genome sequencing it will be difficult to gain access to old samples to be able to update prohibited organisms under re-evaluated classifications.
The proposal I put forward is to use the development of citizen surveillance applications that are being developed for a number of horticultural commodities across Australia to place call outs for samples of oomycete plant pathogens on a regular basis so that a greater number of culture collection samples can be submitted. A regular basis could be every 5 years or based on all diseases of a specific commodity using a similar timeline. Sample bags can be sent to responders with specific instructions to optimise collection and storage quality. Approaching the rural levy provider to fund the sampling and provide advertising would assist in costs associated with the sampling.
The benefits of this proposal:
- Provide enough samples in the collections to allow for DNA extractions without restrictions or as the technology improves.
- Population data on a number of economically important plant diseases. This could be further used for:
- Surveillance data for biosecurity purposes (includes nil results).
- Genotypic information for fungicide resistance projects.
- Information on the lineage of the disease over time, is it moving to more aggressive strains?
- Allow citizens and industry to be included and feel invested in potential scientific research.
- Cost effective way of collecting samples over a wide geographic area.
- Cost effective for the levy providers as it would allow for long term collections rather than the boom and bust cycle of funding large scale projects. Often after large scale projects are completed the samples are destroyed meaning new projects spend money on recollecting samples.
- Provide information as to disease hot spots or location of prevalence over time.
This proposal could be broadened to a wider group of
pathogens but I have written it from the basis of my PhD experience with
oomycetes.