Puccinia graminis genome project Les J Szabo USDA

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

Project team n n n 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 n Puccinia graminis f. sp. tritici CDL 75 -36 -700 -3 (WA) n Avirulent to 25 wheat Sr genes n • Sr 6, Sr 7 b, Sr 8 a, Sr 9 b, Sr 9 d, Sr 10, Sr 11, Sr 13, Sr 14, Sr 22, Sr 24, Sr 25, Sr 26, Sr 27, Sr 28, Sr 30, Sr 31, Sr 32, Sr 33, Sr 34, Sr 35, Sr 36, Sr 37 Parent mapping population n DNA extracted from urediniospores (dikaryotic) n

Genome Sequencing Total reads Q 20 Bases Q 20 Coverage 4 kb plasmid 987, 589 659, 546, 740 8. 24 10 kb plasmid 393, 270 242, 470, 558 3. 03 42 kb fosmid 231, 339 102, 265, 696 1. 28 1, 612, 198 1, 004, 282, 994 12. 55 Totals

Draft assembly n n n n Contig size: 81. 5 mb Super contig size: 88. 6 mb Gaps: 7. 96% No. contigs: 4, 557 No. supercontigs: 392 Percent reads: 60% Q 20 coverage: 6. 8 X

Restriction Fingerprint Map n n n n Pst. I/Eco. RI double digest Ave. fosmid size: 40. 2 kb Ave. number of fragments: 19. 4 Number of clones in map: 22, 249 Estimated clone coverage: 10. 8 X Estimated genome size: 94 mb Number of contigs: 1, 969 Number of singleton clones: 729 (3%)

Restriction Fingerprint Map Number of clones

ESTs Filtered sequences Average length Clones w/2 ends Urediniospores 16, 651 700 9, 980 8, 046 Germinated urediniospores (24 r) 22, 550 688 12, 070 10, 480 Teliospores 18, 026 695 9, 236 7, 325 Total 57, 137 c. DNA library

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

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

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

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

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

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