Decoding the myrtle rust genome, the largest fungal genome (1 Gbp) sequenced to date

Abstract

Austropuccinia psidii, originating from South America, is a globally invasive plant pathogen causing myrtle rust. Several biotypes are recognised, the most widely distributed one known as Pandemic. Unlike many other rust fungi, A. psidii has a very broad host range (currently > 445 myrtaceous species), making it a particularly dangerous plant pathogen. In only 8 years since the Pandemic biotype was first found in Australia, the rust has caused near extinction of at least 3 species (Lenwebbia sp. Main Range, Rhodamnia rubescens, Rhodomyrtus psidioides), caused the decline of at least one keystone species, Melaleuca quinquenervia, and impacted commercial production of Myrtaceae such as the tea-tree (Melaleuca alternifolia) and lemon myrtle (Backhousia citriodora). Critical to combatting this pathogen is understanding the mechanisms it uses to parasitize its many hosts. To enable genomic studies of pathogenicity in A. psidii, we assembled a highly contiguous haplo-phased genome for the pandemic biotype based on PacBio sequence data and scaffolding with Hi-C technology. With a haploid size of just over 1 Gbp, it is the largest assembled fungal genome to date and one of the largest rust genomes known. Annotations based on repeat analysis and post-inoculation mRNA sequence capture from a susceptible host have begun to provide insight into potential infection strategies.