Pyrenophora genome project

Project Information

The Pyrenophora tritici-repentis sequencing project was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant number 2006-55600-16619, and reviewed through the USDA/NSF Microbial Genome Sequencing Project. Our overall goal was to obtain a complete, publicly available genomic sequence of P. tritici-repentis. Our strategy involved Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome was generated using paired end reads from plasmids, and Fosmids and assembled using improved Arachne (3,11).

The sequence generated will provide a genome-wide view of this economically and scientifically important plant pathogen. The information created through this project will help elucidate the underlying molecular mechanisms of pathogenicity (virulence) and disease susceptibility (compatibility). P. tritici-repentis serves as a unique model for resolving these mechanisms, which are currently not well understood. Equally as important, the information created will serve as a basis for research and discovery in controlling the significant disease caused by this plant pathogen. In addition, given that this is the first species from the genus Pyrenophora to be sequenced, the genome of P. tritici-repentis should provide a valuable resource for other grass pathogens in this genus. Finally, sequence data generated from this project will greatly facilitate activities in functional genomics and provide robust sampling of the Pleosporales for comparative genomic studies by the fungal community.

Our specific aims were as follows:

Generate and assemble Pyrenophora genome through whole genome shotgun sequencing.
Integrate the genomic sequence with optical map information.
Perform automated annotation of the sequence assembly.
Immediately release all the information to the public.
Generate ESTs from P. tritici-repentis to improve the annotation of the genome.

This genome project represents a partnership between the Tan Spot Research Community and the Fungal Research Community led by Dr. Lynda Ciuffetti at Oregon State University and the Broad Institute. Dr. Iovanna Pandelova, Oregon State University, provided genomic DNA for the sequence project.

Photo credits:

The photos at the top of the page were kindly provided by (from left to right):

Bill Bockus
Ciuffetti Lab
Ciuffetti Lab
Ciuffetti Lab (DAPI-stained)

Which strain was sequenced?

The strain chosen for sequencing is designated Strain Pt-1C-BFP of race 1. Race 1 is the most prevalent race found in both the US and throughout the world and most of the molecular genetics and applied research has been conducted on race 1 isolates. The first host-selective, protein toxin, Ptr ToxA, was characterized from this race as well (2,16,17,19). Currently, this race is known to produce at least 2 HSTs (1 protein HSTs [Ptr ToxA] and one partially characterized as a low-molecular weight molecule [Ptr ToxC]) (4,5,8,13). In addition, data indicate that there are additional protein toxins produced by this race (17).

Pt-1C-BFP is a fast-growing subculture of isolate Pt-1C. Pt-1C is commonly available and has been used in many laboratories. This isolate grows well both in culture and in planta and has been used in many of the molecular genetic studies. BFP (subculture Pt-1C), as well as, all isolates used for cDNA libraries in this project will be deposited in the Fungal Genetics Stock Center for Community access. All proper USDA/Aphis permits will be obtained.


1. Bailey, K. L. 1996. Diseases under conservation tillage system. Can. J. Plant Sci. 76:635-639

2. Ballance, G.M., L. Lamari, and C.C. Bernier. 1989. Purification and characterization of a host-selective necrosis toxin from Pyrenophora tritici-repentis. Physiol. and Molec. Plant Pathol. 35:203-213.

3. Batzoglou, S., D. B. Jaffe, K. Stanley, J. Butler, S. Gnerre, E. Mauceli, B. Berger, J. P. Mesirov, and E. S. Lander. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Res 12: 177-89.

4. Ciuffetti, L.M. and R.P. Tuori. 1999. Advances in the Characterization of the Pyrenophora tritici-repentis-Wheat Interaction. Phytopathology 89:444-449.

5. De Wolf, E.D., R.J. Effertz, and L.J. Francl. 1998. Vistas of tan spot research. Can. J. Plant Pathol. 20:349-444.

6. Diaz de Ackermann, M. and Kohli, M. M. 1998. Research on Pyrenophora tritici-repentis tan spot of wheat in Uruguay. Pages 134-141 in: Helminthosporium Blights of Wheat: Spot Blotch and Tan Spot. E. Duveiller, H. J. Dubin, J. Reeves, and A. McNab, eds. Mexico, D.F.:CIMMYT.

7. Di Zinno, T., Longree, H., and Maraite, H. 1998. Diversity of Pyrenophora tritici-repentis isolates from warm wheat growing areas: Pathogenicity, toxin production, and RAPD analysis. Pages 302-311 in: Helminthosporium Blights of Wheat: Spot Blotch and Tan Spot. E. Duveiller, H. J. Dubin, J. Reeves, and A. McNab, eds. Mexico, D.F.:CIMMYT.

8. Effertz, R.J., S.W. Meinhardt, J.A. Anderson, J.C. Jordahl, and L.J. Francl. 2002. Identification of a chlorosis-inducing toxin from Pyrenophora tritici-repentis and the chromosomal location of an insensitivity locus in wheat. Phytopathology 92:527-533.

9. Freebairn, D. M. 1986. Stubble: the key to success. Queensland Agric. J. July-August, pp. 194- 195.

10. Hosford, R. M., Jr., Larez, C. R., and Hammond, J. J. 1987. Interaction of wet period and temperature on Pyrenophora tritici-repentis infection and development in wheats of differing resistance. Phytopathology 77:1021-1027.

11. Jaffe, D. B., J. Butler, S. Gnerre, E. Mauceli, K. Lindblad-Toh, J. P. Mesirov, M. C. Zody, and E. S. Lander. 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13: 91-6.

12. Krupinsky, J. M., Halvorson, A. D., and Black, A. L. 1998. Leaf spot diseases of wheat in a conservation tillage study. Pages 322-326 in: Helminthosporium Blights of Wheat: Spot Blotch and Tan Spot. E. Duveiller, H. J. Dubin, J. Reeves, and A., McNab, eds. Mexico, D.F.:CIMMYT.

13. Strelkov SE, Lamari L. 2003. Host-parasite interactions in tan spot [Pyrenophora tritici-repentis] of wheat. Can J Plant Pathol 25:339?349.

14. Sutton, J. C., and Vyn, T. J. 1990. Crop sequences and tillage practices in relation to diseases of winter wheat in Ontario. Can. J. Plant Pathol. 12:358-368.

15. Sykes E.E. and C.C. Bernier. 1991. Qualitative inheritance of tan spot resistance in hexaploid, tetraploid, and diploid wheat. Can. J. Plant Pathol. 13:38-44.

16. Tomas, A., G.H. Feng, G. R. Reech, W.W. Bockus, and J.E. Leach. 1990. Purification of a cultivar-specific toxin of Pyrenophora tritici-repentis, causal agent of tan spot of wheat. Mol. Plant-Microbe Interact. 3:221-224.

17. Tuori, R.P., T.J. Wolpert, and L.M. Ciuffetti. 1995. Purification and immunological characterization of toxic components from cultures of Pyrenophora tritici-repentis. Mol. Plant-Microbe Interact. 8:41-48.

18. Wolpert, T.J., L. D. Dunkle, and L.M. Ciuffetti. 2002. Host-selective Toxins and Avirulence Determinants: What?s in a Name. Ann. Rev. Phytopathol. 40:252-285.

19. Zhang, H.-F., L.J. Francl, J.G. Jordahl, and S.W. Meinhardt. (1997). Structural and physical properties of a necrosis-inducing toxin from Pyrenophora tritici-repentis. Phytopathology 87, 154-160.


Data access and citation

The genome assembly and annotation of Pyrenophora tritici-repentis is available in Genbank and at the JGI Mycocosm site.

Genomic data can also be accessed by ftp via this link

For use of this data, please cite: Manning et al. 2013. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 3(1):41-63. doi: 10.1534/g3.112.004044.