Poplar Rust Fungus Is First Tree Pathogen Sequenced

Rust fungi are a diverse group of plant pathogens composed of more than 120 genera.

The Science

Rust plant pathogens make up a large fungal group that cannot survive on their own, so they use crops as hosts, leading to reduced yields and potentially hindering efforts to grow biomass for fuel. To learn more about these pathogens, a 2006 Community Sequencing Program project at the DOE Joint Genome Institute (JGI) generated the 101-million base pair genome of the poplar leaf rust fungus Melampsora larici-populina, the first tree pathogen sequenced.

The fungal project complements work as poplar leaf rust outbreaks weaken poplar trees, a candidate bioenergy feedstock whose genome sequence was published by JGI in 2007. A new study that involved a JGI researcher compares the genomes of poplar leaf rust and wheat stem rust fungi, the latter sequenced by the Broad Institute, in order to develop better biocontrol methods. In combination with the genome sequence of Populus, published in 2006, researchers will be able to compare and dissect the molecular interactions that lead to symbiotic versus pathogenic responses in the host plant.


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. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. 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. A deeper understanding of the complex array of the factors, including effector-like small secreted proteinss, affecting host–pathogen interactions and coevolution could enable efficient targeting of parasite-control methods in agricultural and forest ecosystems.

Principal Investigator

Francis Martin
Nancy Université

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Duplessis, S., et al. 2011. “Obligate Biotrophy Features Unraveled by the Genomic Analysis of Rust Fungi,” PNAS Early Edition. DOI:10.1073/pnas.1019315108.