New Insights into the Genome 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. The effects of Repeat-Induced Point mutations (RIP) was evident with a 4.24:1 ratio of transitions:transversions seen. The majority (75%) of SNPs were predicted up- and downstream of genes and only 6.03% of SNPs displayed modifying effects within genic regions.  Even higher conservation was observed at splice sites and start codons, with only 0.11% of modifying SNPs seen in these regions. 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. 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.