Fusarium oxysporum is a species complex of endophytes, saprophytes and phyto-pathogens. There are more than 150 formae speciales affecting more than 100 plant species of important agricultural crops such as banana, tomato, legumes amongst others and is ranked fifth out of top ten most important plant pathogens based on scientific and economic importance.
Fusarium oxysporum formae speciales are often polyphyletic, making it impossible to identify them on the basis of conserved genes. Currently there are few consistently reliable molecular ways of differentiating between pathogens, endophytes and saprophytes and no easy way of discriminating endemics from exotics. The ability of the fungus to undergo recombination is another hurdle to molecular diagnostics. Although a lot of putative effectors have been characterised, SIX genes have been studied and used more widely to discriminate formae speciales but still cannot discriminate between all, or separate pathogenic strains from others.
In order to devise a rapid robust diagnostic protocol for this important horticultural pathogen, one needs to understand the genetic basis of host specificity and virulence which can only be achieved via whole genome sequencing.
The aim of the project is to carry out whole genome sequencing of Fusarium oxysporum specimens of horticultural crops maintained in the Victorian Plant Pathogen Herbarium (VPRI) using a combination of Illumina HiSeq and PacBio RS platforms. Single molecule real time (SMRT) sequencing technology used by PacBio RS will be used for scaffolding, gap filling and genome sequence finishing of the sequence derived from Illumina HiSeq. Both ab initio and evidence-based methods will be used for effector prediction, which will be used to characterise the Fusarium oxysporum specimens in the herbarium.