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 is to obtain a complete, publicly available genomic sequence of P. tritici-repentis. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is 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 are 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.
Who provided the photos for this website?
The photos were kindly provided by (from top to bottom):
- Bill Bockus
- Ciuffetti Lab
- Ciuffetti Lab
- Ciuffetti Lab (DAPI-stained)
Which strain is 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.
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