Unravelling rust fungi genetic programs through life cycle transcriptomics – RustCyclomics

Rust fungi (Pucciniales) are plant pathogens causing rust diseases in many crops and trees and are a serious threat to agriculture. They are obligate biotrophs and as such, they are particularly hard to study in laboratory conditions. The Pucciniales have unique biological features compared to other fungi, such as very complex life cycles and peculiar genomic profiles. Notably, they alternate on two taxonomically unrelated hosts and form five distinct types of spores successively in a year with a dormancy phase. Compare to other fungi, the rusts display remarkably large genome sizes, a large amount of repeat elements and large gene numbers. Strikingly, about half of these genes are unique to the order Pucciniales with no known function so far. The basis of the RustCyclomics project comes from the concomitant observation of i) a significant amount of unknown genes in a major taxonomical order of plant pathogenic fungi threatening agriculture and ii) the complexity of a life cycle which remains largely unexplored. Our hypothesis is that the use of state-of-the-art omics approaches will help to unravel the genetic programs of Pucciniales. The rust fungus Melampsora larici-populina infecting poplar and larch is the most advanced model among rust pathosystems. We aim to explore its life cycle through an extensive transcriptomics approach targeting major stages of the cycle, i.e. host infection, asexual/sexual reproductions and dormancy. Such a dissection will allow to identify stage-specific gene expression profiles, as well as putative regulatory elements through interaction network analysis. We aim to combine these findings with protein structure modeling using the most recent Artificial Intelligence-based approach. Unravelling genetic programs will pinpoint putative functions of unknown genes allowing to better understand the peculiar biology of rust fungi and provide new targets to combat rust diseases.