Puccinia graminis genome project

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Puccinia graminis genome project

• Les J Szabo
• USDA ARS Cereal Disease Lab
• Department of Plant Pathology
• University of Minnesota

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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

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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)

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Genome Sequencing
Total reads Q20 Bases Q20 Coverage
4kb plasmid 987,589 659,546,740 8.24
10kb plasmid 393,270 242,470,558 3.03
42kb fosmid 231,339 102,265,696 1.28
Totals 1,612,198 1,004,282,994 12.55
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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

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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)

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

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Assignment of unigenes
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Assignment of unigenes
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Summary

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

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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

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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