Unravelling the complex life cycle of rust fungi through genomics

Abstract :

Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi with alternation of generations, development of up to five different sporulating stages, and, requirement of infecting two unrelated host plants for many species [1]. We developed a multidisciplinary project bringing together various disciplines (i.e. molecular biology, genomics, population genetics, protein biochemistry) to unravel the complex life cycle and biology of the poplar rust fungus Melampsora larici-populina. 

In this presentation, I will first provide a brief overview of the major progress we made in the past ten years in deciphering the mechanisms of interaction in the model forest pathosystem poplar-Melampsora (unravelling candidate rust fungi effectors and components of the poplar immune response), then I will address our most recent progress achieved on the front of genomics, including : 

i) the generation of telomere-to-telomere phased genomes for several Melampsora spp. and detailed annotation of transposable elements to better understand how these mobile elements impact genome organization and evolution [2]; 

iii) life cycle transcriptomics to better understand the biology of M. larici-populina by studying gene families related to biotrophy and virulence and by targeting genes of unknown functions [1,3]. 

Taken together, these advances provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.

[1] Duplessis et al. (2021) Host adaptation and virulence in heteroecious rust fungi. Annual Review of Phytopathology, doi: 10.1146/annurev-phyto-020620-121149.

[2] Corre et al. (2025) Ancestral and recent bursts of transposition shaped the massive genomes of plant pathogenic rust fungi. BioRxiv, doi : 10.1101/2025.01. 10.632365, BMC Genomics (In Press).

[3] Guerillot et al. (2021) A comprehensive collection of transcriptome data to support life cycle analysis of the poplar rust fungus Melampsora larici-populina. BioRxiv, doi: 10.1101/2021.07. 25.453710.