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

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Presentation transcript:

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 Jacquie Schein, Genome Sciences Centre, BC Cancer Agency Funding: NSF Microbial Genome Sequencing Program

Genome Sequencing Puccinia graminis f.sp. tritici CDL (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)

Genome Sequencing Total readsQ 20 Bases Q 20 Coverage 4kb plasmid987,589659,546, kb plasmid 393,270242,470, kb fosmid231,339102,265, Totals1,612,1981,004,282,

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

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%)

Restriction Fingerprint Map Number of clones

ESTs cDNA library Filtered sequences Average length Clones Clones w/2 ends Urediniospores16, ,9808,046 Germinated urediniospores (24r) 22, ,07010,480 Teliospores18, ,2367,325 Total57,137

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%

Assignment of unigenes Ured 24h_Ured Telio All assembled genes

Assignment of unigenes Ured 24h_Ured Telio All assembled genes 63(38) Ured 24h_Ured Telio Annotated genes only (number of assigned GO categories) 17(21)57(35) 5 (12) 15 (20) 138(40) 30(24)

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

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

People 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