Using Bioinformatics Tools to Study the Genomic Diversity of the Plant Pathogen Leptosphaeria maculans in Australia

Blackleg, caused by the fungal pathogen Leptosphaeria maculans, is a devastating disease affecting canola (Brassica napus), a food crop worth $2.5 billion to the Australian economy. Blackleg can lead to 15% average crop losses, and up to 90% per year. Next generation sequencing (NGS) technology enables us to scrutinise organisms at the genomic level, including gene loss and presence-absence variation (PAV) analysis to identify various characteristics of a genome. Here we present gene loss and PAV analysis to study the genomes of blackleg isolates. Gene loss identifies disposable genes and genes that are essential to the survival of the pathogen. PAV identifies unique reads between samples, and does not require a reference genome sequence. Selection pressure to evolve against host resistance can also be determined using these analyses. Novel Avirulence (Avr) gene candidates, which interact in a gene-for-gene manner with resistance genes in Brassica species, have been identified, along with validation of known Avr genes. We found that up to 8 genes were lost uniquely in some isolates, with 15 genes lost in common among all isolates analysed. These methods are also being used to characterise the genomic diversity of the pathogen and to identify the difference in selection pressure in various regions of the genome, providing insights into the genome variation and function within this pathogen. Genomic information about this pathogen will better equip us to manage blackleg disease and reduce future crop losses.