We are a highly collaborative and interactive team that studies the interaction of fungi and plants. We use a wide variety of tools reaching from biochemistry, bioinformatics, genomics, to environmental sampling. Modern biology is best mixed by combining good ‘old school’ biochemistry with modern data science stirred with interesting biological questions.
Please see How to Join for more information.
Our team focuses on questions around plant biosecurity in Australia by studying the interaction between plants and their fungal pathogen. Specifically, we work on agronomic important wheat rust fungi and the environmental important myrtle rust fungus that infects a wide range of myrtacea (e.g. eucalyptus trees). We also have an interest in bioinformatics and sequencing technologies in relation to plant sciences, and are currently doing research into MinION sequencing ability and error.
Key questions are:
Many of these questions are also applicable to other study systems, hence we are a really collaborative team. We work with other groups at RSB and beyond on plant, animal, and fungal genomics.
We study plant-fungi interactions on multiple molecular and temporal scales. This includes many aspects:
Our 2019 lab projects include:
Fungal genomics, evolution, and host adaptation (Summer, Honours, Master, and PhD students)
Detection of fungal pathogens and their associated microbiome (Summer, Honours, and Master students)
Our experience with MinION sequencing:
Evolution has driven genetic diversity of life on Earth, but also created highly complex genomes that are difficult to sequence. Current draft genomes can have thousands to hundreds of thousands of contigs rather than chromosomes, containing incorrect assemblies, gaps and errors. With rapid advances in long-read technologies, it is becoming possible to resolve complex genomes, including repetitive, polyploid plant genomes. Despite the technology being available, a challenge persists: the extraction of pure high molecular weight DNA suitable for long-read sequencing. This is particularly true of recalcitrant native Australian trees such as Eucalypts and Acacias. To resolve this, firstly we optimised a density gradient based nuclei extraction to remove cytoplasmic secondary metabolites, phenols and limit reads from high copy count plastid genomes. Secondly, we optimised a gentle high molecular weight DNA extraction free of columns and high centrifugation, to limit DNA fragmentation. Finally, the DNA was purified and size selected by gel electrophoresis. For sequencing, we adopted the portable MinION sequencer from Oxford Nanopore Technologies. Using these approaches, we have been obtaining approximately 10 gigabases of sequencing from a single MinION revC flow cell and approximately 15 gigabases with new revD flow cells. This includes quality reads over 200 kb in length, average N50 values of 20 kb and some N50 values exceeding 45 kb. Such ultra-long reads assist the assembly of high quality genomes, from telomere to telomere.
Beyond being nerds, we aim to contribute to a welcoming and progressive academic environment. Group members are actively encouraged to contribute to community events, outreach science communication, and university commities. For example, group members are part of eLife’s Early Career Advisory Board, ambassador for the protocol sharing webpage protocols.io, and chair of the RSB Equity Committee. And of course we love open access and reproducible science. For more information and detail on our contributions to open science, please look at our Open Science page.
|Granted to||When||What||Grant type||Amount (AUD)||Role|
|B. S.||02/2019||Mozilla Science Foundation, Reproducibility for Everyone||Science Grant||$15k||Principal Investigator|
|B. S.||11/2018||Research School Biology, Increasing Scientific Rigor at RSB||Science Grant||$10k||Principal Investigator|
|B. S.||10/2018-09/2022||Australian Research Council - Identify, characterise, detect factors causing wheat disease epidemics||Research Grant||$780k||Principal Investigator|
|B. S.||07/2017-06/2019||Hermon Slade Foundation, Rapid detection and diagnosis of plant pathogens||Innovation Grant||$50k||co-Principal Investigator|
|B. S.||05/2015-04/2017||Bioplatform Australia, Sequencing grant for wheat stripe rust fungi||Sequencing Grant||$30k||co-Principal Investigator|
|B. S.||09/2015-09/2018||Australian Research Council, Understanding the genomic and epigenomic mechanisms driving the evolution of highly virulent stripe rust races||Research Grant||$350k||Principal Investigator|
|B. S.||07/2012-09/2015||Human Frontier Science Program Long-Term Fellowship, Function of non-RD kinases in plant immunity||Postdoctoral Grant||$195k||Principal Investigator|
|B. S.||01/2012-07/2015||European Molecular Biology Organization Long-Term Fellowship, Function of non-RD kinases in plant immunity||Postdoctoral Grant||$80k||Principal Investigator|
|Awarded to||When||Award type||What|
|B. S.||10/2018-09/2022||Fellowship||Future Fellowship 2018 - Australian Research Council|
|B. S.||01/2017||Award||Shortlisted for the New Phytologist Tansley Medal for Excellence in Plant Science|
|B. S.||10/2015-09/2018||Award||Discovery Early Career Researcher Award - Australian Research Council|
|B. S.||07/2012-09/2015||Fellowship||Human Frontier Science Program Long-Term Fellowship|
|B. S.||01/2012-06/2012||Fellowship||European Molecular Biology Organization Long-Term Fellowship|
|B. S.||07/2011||Award||John Innes Foundation Prize for Excellence in Scientific Research|
|B. S.||10/2006-09/2010||Scholarship||Rotation PhD Scholarship John Innes Centre and The Sainsbury Laboratory|
|B. S.||09/2006||Award||Short-listed for the SET Student of the Year Awards in 2006|
|B. S.||07/2006||Scholarship||Plant Science Scholarship of the University of Glasgow|
|B. S.||06/2005||Scholarship||Lang Scholarship (Botany) of the University of Glasgow|
|B. S.||05/2005-06/2006||Scholarship||Sainsbury Undergraduate Studentship in Plant Science|
|B. S.||10/2002-07/2006||Scholarship||Scholarship for Intellectually Gifted People of the State of Bavaria|
|B. S.||09/2002-09/2010||Scholarship||Scholarship of e-fellows.net|