Aspergillus fumigatus is a ubiquitous pathogenic mould found in the environment. This fungus is the species most frequently responsible for invasive aspergillosis disease, a serious infection with a high mortality rate responsible for over 1.5 million deaths annually. A. fumigatus possesses phenotypic variations among its strains, including in the degree of virulence. Pangenomic studies on A. fumigatus have hypothesised that these differences could come from the wide variation in gene content among strains. This includes a large number of accessory genes that are specific to subpopulations of A. fumigatus and represent 30% of the pangenome. Due to their absence in the main reference strains, most of these genes are not yet functionally characterised.

To better understand the functional role of these uncharacterised genes, we have created a pangenome reference of A. fumigatus that encodes the entire gene collection of the species and their variation. This novel tool can be used as a reference for genomic and transcriptomic analyses. To construct the pangenome reference, we used a representative collection of 15 isolates' long-read sequence data that we de novo assembled into near chromosomal assemblies. Individual genomes were combined into a pangenome graph, and the gene annotations were imposed onto the graph. This reference pangenome encapsulates the diversity of A. fumigatus by including genes absent from the linear reference Af293 and opens new perspectives to describe these genes functionally. By using this new reference with transcriptomic data, we aim to understand the role of the accessory genome and intraspecies diversity in the virulence and phenotypic differences of A. fumigatus.