Better plant quarantine enabled by Galaxy Australia’s two millionth job

Plants grown at the Post Entry Quarantine facility in Mickleham, Victoria (Photo: Robin Eichner, DAWE)

To celebrate the broad uptake and diversity of their users, Galaxy Australia took the opportunity to spotlight the researcher who submitted the two millionth job to the service. 

Dr Ruvini Lelwala is a Bioinformatics Research Associate at the Queensland University of Technology (QUT). However Ruvini is based at the other end of the country at the Post Entry Quarantine (PEQ) Facility in Mickleham, Victoria, which importantly places her where high-risk plant material undergoes quarantine after importation into Australia. 

Working within a multidisciplinary group of bioinformaticians, computational biologists, molecular biologists, plant pathologists and policy makers, Ruvini’s PhD in plant pathology is put to good use as the team develops enhanced diagnostics for the detection of exotic plant pathogens.

Under the guidance of A/Prof Roberto Barrero, eResearch Office (QUT), Ruvini and bioinformatician Dr Marie-Emilie Gauthier work closely with the Australian Department of Agriculture, Water and the Environment (DAWE) Science and Surveillance Group at PEQ while liaising with a wider community from QUT, DAWE, Agriculture Victoria, Hort Innovation and New Zealand Ministry for Primary Industries.

Roberto’s team has developed a novel bioinformatics toolkit – Virus and Viroid Surveillance and Diagnosis (VSD) toolkit, which can be used to detect viruses and viroids from host plant RNA extracts. High Throughput Sequencing (HTS) enables the rapid detection of viruses and viroids in imported plant material in a single test and can accelerate the release of plant genetic stocks held at PEQ facilities. 

eResearch@QUT provides access to research tools and end-to-end analytical workflows that run on diverse compute resources, enabling reproducible large-scale processing of plant biosecurity samples. The team also partners with Galaxy Australia to provide a bioinformatics training interface for staff at PEQ.

Galaxy Australia is useful in the development and implementation of their VSD pipeline through creating dataset collections, databases, automated workflows, quality control of sequencing reads, targeted genome assembly, finding open reading frames, and sequence similarity searches, amongst other tasks. 

I can seamlessly submit multiple jobs to Galaxy Australia that can be queued and run in parallel on multiple ‘histories’. Moreover, there’s a good support team if I ever need help with troubleshooting.

Dr Ruvini Lelwala, QUT

The Galaxy Australia ‘tool shed’ already has the majority tools needed, but Ruvini simply requests that new ones are added as required. Galaxy Australia is an active contributor to the global repository of analytical tools and encourages its users to explore the potential of over 8,000 tools to boost their analytical options.

Ultimately they aim to recreate the VSD pipeline on Galaxy Australia, implement the pipeline in real-time and train PEQ molecular biologists to use the pipeline to process and analyse HTS datasets. Galaxy Australia enables the team to provide access to specialised plant viruses/viroids diagnosis pipelines to their collaborators who do not have formal training in bioinformatics. The platform helps upskill molecular biologists thanks to its user-friendly Graphical User Interface and the availability of supportive training materials. 

The long-term goal is to use Galaxy Australia to facilitate routine quarantine testing of imported plants using HTS technologies. The potential impact on Australia's horticulture sector of faster access to new plant stock has been documented previously in QUT’s Using next generation genetic testing to give growers a competitive boost.   

The two projects using Galaxy Australia are:

MT18005 ‘Improving access to new germplasm through faster and more accurate diagnostics’ funded by Hort Innovation using the Hort Innovation Citrus, Grape Tables, Rubus, Potato and Nursery research and development levy, co-investment from Queensland University of Technology and contributions from the Australian Government. Hort Innovation is the grower-owned, not-for-profit research and development corporation for Australian horticulture.  

BIP202048 ‘Transformation of exotic plant disease testing at PEQ, Mickleham by implementation of high-throughput sequencing’, is funded by the Department of Agriculture, Water and the Environment (DAWE) Biosecurity Innovation Program. 

For further information contact:
A/Prof. Roberto Barrero
eResearch Office, Queensland University of Technology
roberto.barrero@qut.edu.au