Patterns of Gene Loss in Population Genomic Data - Identifying Disposable Genes

Blackleg, caused by the fungal pathogen Leptosphaeria maculans is a devastating disease affecting canola plants (Brassica species), leading to significant economic losses every year. Effective and sustainable methods must be developed to manage this disease. Next generation sequencing (NGS) technology provides a variety of tools that enable us to scrutinise any organism at the genomic level. This high throughput genomic sequence data can be used for gene loss and presence-absence variation analysis to identify various characteristics of a genome. Here we present gene loss and presence absence variation analysis used to study the genomes of blackleg isolates. 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 AvrLm1, AvrLm4-7 and AvrLm6. We found that up to 8 genes were lost uniquely in some isolates, with 15 genes lost in common among all isolates analysed. Of the 76 supercontigs (SC) of the blackleg genome, SC13 followed by SC12 reported most genes being lost. Both 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.