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Puccinia graminis genome project

Puccinia graminis genome project. Les J Szabo USDA ARS Cereal Disease Lab Department of Plant Pathology University of Minnesota. Project team. Les J Szabo - USDA ARS CDL, UMN Christina Cuomo, Broad Institute, MIT Ralph Dean, CIFR, NCSU

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Puccinia graminis genome project

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  1. Puccinia graminis genome project Les J Szabo USDA ARS Cereal Disease Lab Department of Plant Pathology University of Minnesota

  2. Project team • Les J Szabo - USDA ARS CDL, UMN • Christina Cuomo, Broad Institute, MIT • Ralph Dean, CIFR, NCSU • Jacquie Schein, Genome Sciences Centre, BC Cancer Agency • Funding: NSF Microbial Genome Sequencing Program

  3. Genome Sequencing • Puccinia graminis f.sp. tritici • CDL 75-36-700-3 (WA) • Avirulent to 25 wheat Sr genes • Sr6, Sr7b, Sr8a, Sr9b, Sr9d, Sr10, Sr11, Sr13, Sr14, Sr22, Sr24, Sr25, Sr26, Sr27, Sr28, Sr30, Sr31, Sr32, Sr33, Sr34, Sr35, Sr36, Sr37 • Parent mapping population • DNA extracted from urediniospores (dikaryotic)

  4. Genome Sequencing

  5. Draft assembly • Contig size: 81.5mb • Super contig size: 88.6mb • Gaps: 7.96% • No. contigs: 4,557 • No. supercontigs: 392 • Percent reads: 60% • Q20 coverage: 6.8X

  6. Restriction Fingerprint Map • PstI/EcoRI double digest • Ave. fosmid size: 40.2kb • Ave. number of fragments: 19.4 • Number of clones in map: 22,249 • Estimated clone coverage: 10.8X • Estimated genome size: 94mb • Number of contigs: 1,969 • Number of singleton clones: 729 (3%)

  7. Number of clones Restriction Fingerprint Map

  8. ESTs

  9. ESTs preliminary analysis • 3,442 ESTs • Urediniospore - 1,149 • Germinated urediniospores - 1,146 • Teliospores - 1,147 • 1,632 unigenes • 457 contigs • 1,175 singleton • 325 unigenes could be annotated • 20%

  10. 442 94 357 Ured 24h_Ured 31 41 51 Telio 616 All assembled genes Assignment of unigenes

  11. 17(21) 57(35) 63(38) Ured 24h_Ured 5 (12) 442 94 357 30(24) Ured 15 (20) 24h_Ured 31 41 Telio 51 138(40) Telio 616 Annotated genes only (number of assigned GO categories) All assembled genes Assignment of unigenes

  12. Summary • 12X genome sequence • Draft assembly released Jan 2007 • Restriction fingerprint map and assembled genome sequence are highly similar (99%)

  13. Summary • 57,000 EST reads • Three libraries • Urediniospores • Germinated urediniospores (24hr) • Teliospores • Preliminary analysis of 3,300 ESTs • 1,632 unigenes • 325 were able to be annotated • Each of the three libraries represent distinctly different sets of transcripts

  14. USDA ARS CDL, University of Minnesota Les J Szabo Jerry Johnson Charlie Barnes Kim-P. Nguyen Broad Institute, MIT Christina Cuomo CIFR, NCSU Ralph Dean Doug Brown Funding: NSF Microbial Genome Sequencing Program Genome Sciences Centre, BC Cancer Agency Jacquie Schein University of Hawaii Shaobin Zong People

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