Understanding Genome Structure and Diversity of the Plant Pathogen, Leptosphaeria maculans

Leptosphaeria maculans is a significant pathogen of Brassica species and causes Blackleg; the most economically damaging disease in the important crop canola. Next generation sequencing technology has allowed a high throughput method of generating genomic sequence data in many important pathogens such as L. maculans. Using blackleg NGS data over 21,000 SNPs were identified genome-wide. An analysis of Presence-Absence Variations (PAVs) within further L. maculans isolates was conducted. Using this method, we show that the presence/absence of avirulence genes, important in the gene-for-gene interaction with resistance genes in Brassica species, can be validated with PAV analysis. In addition, genomic regions that are variable between different L. maculans have been identified to determine the extent of selection pressure on these regions in the genome. Of particular interest is the identification of novel avirulence gene candidates which was completed using this method, whereby PAVs from these isolates with different avirulence gene composition were compared. A comparison of NGS data using a novel heuristic gene-loss prediction in L. maculans revealed a number of regions that are similarly present in some isolates and absent in others. This method relied on determining the coverage of NGS sequence tags across the annotated L. maculans genome and allowed for a clearer idea on which genes are essential and non-essential for survival of the organism. These analyses provide new insights into the genome variation and function within this pathogen. Understanding the genome of L. maculans will provide information on developing effective and sustainable approaches to managing blackleg disease.