Puccinia Comparative Genomic Projects

Project Information

Rust fungi (Pucciniales) cause some of the most devastating plant diseases and are comprised of more than 7,000 species in over 100 genera (1,2). The genus Puccinia is the largest in the Pucciniales and is considered the most economically destructive genera of biotrophic fungi (3). Members of this genus are serious pathogens on all major cereal crop species except rice. Some examples are Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust (black rust); P. striiformis f. sp. tritici, wheat stripe rust (yellow rust); P. triticina, wheat leaf rust (brown rust). Cereal rust fungi are well suited to incite serious epidemics because they can produce large numbers of infectious spores (urediniospores) that are adapted for aerial transport and the crops they infect are often grown contiguously over large acreages. In 1999, a new highly virulent race TTKSK (Ug99) of P. graminis was identified in Uganda, and since then has spread, causing a widening epidemic in Kenya and Ethiopia (4). We have sequenced the genomes of P. graminis f. sp. tritici, P. triticina, and P. striiformis f. sp. tritici.

Funding for the P. graminis sequencing project was provided by the National Science Foundation and for P. triticina and P. striiformis by the USDA Cooperative State Research, Education and Extension Service through the Microbial Genome Sequencing Program.
P. graminis

For Puccinia graminis, genomic DNA from strain CRL 75-36-700-3 (race SCCL) was prepared from urediniospores (which are dikaryotic) by the Szabo group at the University of Minnesota. The genome was sequenced using ABI (Sanger) technology to generate paired-end reads from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. A physical fingerprint map was generated using the shotgun Fosmid library. We also constructed cDNA libraries from urediniospores, haustoria, uredinial hyphae, and pycnial/aecial tissues (from infected barberry).  RNA-Seq was used to update the predicted gene set.

For Puccinia triticina, genomic DNA from isolate 1-1 of Race 1 (BBBD) was prepared from urediniospores (which are dikaryotic) by the Fellers group. RNA samples for sequencing were prepared by the Bakkeren, Fellers, and Szabo groups. The genome was sequenced using a hybrid of ABI (Sanger) Fosmid-end two 454 libraries (fragment and 3kb inserts). BAC-end sequence was generated using Sanger technology by the Michael Smith Genome Sciences Centre in Vancouver. The gene set was informed by EST and RNA-Seq data.

For Puccinia striiformis, genomic DNA from isolate 2K41-Yr9 race PST-78 (Great Plains, 2000) was prepared from urediniospores (which are dikaryotic) by the Chen group. RNA samples for sequencing will be prepared by the Chen and Hulbert groups and by Zhensheng Kang (Northwest A&F University, China).  The genome was sequenced using a hybrid of 454 and either 454, Sanger, or Illumina Fosmid-end sequence. The gene set was informed by EST and RNA-Seq data.

Project Leadership

P. graminis

Les Szabo, USDA-ARS, Univ. of Minnesota, St Paul, MN
Christina Cuomo, Broad Institute
Ralph Dean, North Carolina State University
Jacqueline Schein, British Columbia Cancer Agency Genome Sciences Centre

P. triticina

Christina Cuomo, Broad Institute
Guus Bakkeren, Agriculture & Agri-Food Canada, Summerland, BC
John Fellers, USDA-ARS, Manhattan, KS
Les Szabo, USDA-ARS, Univ. of Minnesota, St Paul, MN

P. striiformis

Christina Cuomo, Broad Institute
Xianming Chen, USDA-ARS Wheat Genetics, Quality, Physiology, and Disease Research Unit, and Department of Plant Pathology, Washington State University
Scot Hulbert, Department of Plant Pathology, Washington State University

What are rust fungi?

The rust fungi are highly destructive plant pathogens, and are obligate on their plant host. Within the fungal kingdom, they are found within phylum Basidiomycota and subphylum Pucciniomycotina, which contains approximately one-third of all described Basidiomycete species.

Puccinia is the largest genus of rust fungi and currently contains approximately 4,000 species. P. graminis, P. triticina, and P. striiformis represent distinct lineages within the cereal and grass rusts.

What is Puccinia graminis?

Puccinia graminis, the causal agent of stem rust, has caused serious disease of small cereal grains (wheat, barley, oat, and rye) worldwide. P. graminis is the first sequenced representative of the rust fungi. Stem rust of wheat has been a serious problem wherever wheat is grown and has caused major epidemics in North America. In 1999, a new highly virulent race TTKS (Ug99) of P. graminis was identified in Uganda, and since then has spread, causing a widening epidemic in Kenya and Ethiopia. Due to its devastating ability to cause epidemics, P. graminis was developed as a biological warfare agent during the Cold War and is now considered one of the most important potential agricultural bio-terrorism threats to U. S. agriculture.

Puccinia graminis is a heteroecious rust fungus with five spore stages and two hosts. The asexual stage (uredinial) infects cereal and grass hosts and is the economically important form of the pathogen. The sexual stage begins in the resting spore (teliospore) on leaves and stalks of the gramineous host. The sexual stage is completed on the aecial (alternate) host, barberry. P. graminis, as a species, has a broad host range that includes more than 300 species of cereals and grasses. Wheat stem rust, P. graminis f.sp. tritici is known to naturally infect 28 species belonging to eight genera, including wheat, barley and rye.

What is Puccinia triticina?

Puccinia triticina, the causative agent of wheat leaf rust (also known as brown rust of wheat), is one of the most serious diseases of wheat in North-America and throughout the world. Severe epidemics caused by leaf rust plague North-American wheat production. Wheat resistance to cereal rusts is precarious at all times, as new races evolve regularly and threaten sustainable crop production. Genetic resistance remains the most economical and environmentally sound method of minimizing yield losses due to rust fungi, but development of wheat cultivars with long-lasting leaf rust resistance has been complicated by the highly variable nature of P. triticina.

P. triticina has a complex life cycle which includes five different spore types and two hosts, wheat and its alternate host meadow rue (Thalictrum speciosissimum) on which it completes its sexual stage. The asexual uredinial stage on wheat is the economically important part of the life cycle which can progress from initial infection to sporulation within ten days under warm and humid conditions, potentially leading to epidemics. During infection on wheat, the pathogen undergoes a high degree of morphological and physiological differentiation. After landing on a wheat epidermis, the dikaryotic urediniospore germinates within hours when sufficient moisture is available. Germination and formation of infection structures are affected by chemical, temperature and surface contact responses. The emerging germ tube extends until a stomatal pore is encountered. Thigmotropic responses to the topology of the leaf surface and negative phototropism help direct the germ tube to a stoma where an appressorium is produced over the stomatal aperture.

What is Puccinia striiformis?

Puccinia striiformis Westend. f. sp. tritici Eriks. (Pst) causes stripe rust, an important disease of wheat worldwide. Other formae speciales of P. striiformis cause stripe rust of barley or other grasses. Stripe rust is most prevalent in cool regions of the world where most of the world's wheat and barley are produced. Because stripe rust is favored by low temperatures, the disease occurs earlier in the growing season than leaf and stem rusts, and therefore, has potential to cause more damage. Pst has become increasingly important in the U.S. where epidemics since 2000 have caused yield losses of over 246 million bushels in spite of millions of dollars spent on fungicides.

Unlike P. triticina and P. graminis, the Pst lifecycle consists of uredinial, telial, and basidial stages; pycnial and aecial stageshave not been found. The fungus produces one-celled, dikaryotic (n+n) urediniospores-containing yellow to orange-colored uredia on leaves, leaf sheaths, and glumes of wheat or other grasses. Urediniospores are airborne and infect wheat and grasses, and produce new urediniospores. The growth and reproduction of the fungus within the plant tissue destroys leaf area and utilizes water and nutrients from the host plant, which inhibits growth and desiccates the plant, reducing grain yield and quality. Later in the season, black telia may form along uredia. Teliospores produced in telia are diploid (2n) and two-celled, which can germinate to form one-celled and haploid (n) basidiospores. Because Pst has no known alternate hosts, basidiospores have no known function in the pathogen lifecycle.

Pst populations change their virulence amazingly rapidly by mechanisms that are largely unknown. Pst is recalcitrant to classical genetic manipulations because it is an obligate biotroph without a known sexual stage.

Photo captions and credits

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Two-celled teliospores of Puccinia graminis f. sp. tritici, the cause of stem rust of wheat. Photo courtesy J. F. Hennen
P. graminis teliospores. Courtesy of Yehoshua Anikster and Tamar Eilam, Tel Aviv University.
Wheat Stem Rust. Courtesy of the Agricultural Research Service, USDA.
Puccinia triticina aeciospore pustules on leaves of the alternate host, meadow rue or Thalictrum speciosissimum. Photo by Drs. Yehoshua Anikster and Tamar Eilam, Tel Aviv University, Israel.
Wheat leaf showing P. triticina urediniospores pustules. Photo by Brent McCallum, Agriculture & Agri-Food Canada, Winnipeg, BC


Aime, et al., 2006. An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98:896-905.
Cummins, GB and Hiratsuka, Y. 2003. Illustrated genera of rust fungi. Third Edition. APS Press, St. Paul.
Hooker, AL. 1967. The genetics and expression of resistance in plants to rusts of the genus Puccinia. Annu Rev Phytopathol 5:163-182.
Borlaug Global Rust Initiative

Data access and citation

The genome assemblies and annotation of are available in Genbank: Puccinia graminis, Puccinia triticina, and Puccinia striiformis.  Genomes are also available and at the JGI Mycocosm site.

Genomic data can also be accessed by ftp via this link.

For use of the P. graminis data, please cite: Duplessis et al. 2011. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. PNAS 108(22):9166-71.