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Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101 mega base pair genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89 mega base pair genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,841 predicted proteins of M. larici-populina to the 18,241 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic life-style include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins (SSPs), impaired nitrogen and sulfur assimilation pathways, and expanded families of amino-acid, oligopeptide and hexose membrane transporters. The dramatic upregulation of transcripts coding for SSPs, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells

National audience; The genome of the poplar rust fungus Melampsora larici-populina has been sequenced almost 10 years ago by an international consortium in the frame of the Community Sequencing Program of the US DoE Joint Genome Institute. The detailed analysis of the genome content and gene annotation, along with comparison to the cereal rust fungus Puccinia graminis f.sp. tritici, has revealed the singular profile of rust fungal genomes. Similar to other obligate biotrophic fungi (e.g. powdery mildews), rust fungi exhibit a large genome size (>80Mb) and an important content in repeat elements (~45%). In contrast, they possess a large gene complement (>15,000 genes) marked by the presence of many expanded gene families specific to the Pucciniales order or the corresponding families (i.e. Melampsoraceae or Pucciniaceae). Since, more rust genomes have been sequenced, analyzed and published, confirming these general trends and opening great perspectives for comparative rust genomics. The genome of M. larici-populina has been instrumental to explore the genetic diversity of the fungus through re-sequencing of isolates sampled through the years in natural populations. Beside, gene expression during poplar leaf infection or throughout the life cycle has helped to build a comprehensive transcriptomic analysis of the rust fungus. More recently, a genetic map of the poplar rust fungus has been obtained from a self-cross of the reference genome isolate. All these data have led to the version 2 of the genome now anchored to 18 linkage groups, including a refined gene annotation available online on the MycoCosm website. We will provide here a complete update on the poplar rust genome and an overview of ongoing works to decipher the biology of this fascinating and devastating rust fungus.