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Analysis of the bread wheat genome using whole -genome shotgun sequencing Manuel Spannagl

Analysis of the bread wheat genome using whole -genome shotgun sequencing Manuel Spannagl MIPS, Helmholtz Center Munich. Wheat - why bother ?. Many varieties incl. bread wheat , durum („ pasta “) wheat …

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Analysis of the bread wheat genome using whole -genome shotgun sequencing Manuel Spannagl

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  1. Analysis ofthebreadwheatgenomeusingwhole-genome shotgunsequencing Manuel Spannagl MIPS, Helmholtz Center Munich

  2. Wheat- whybother? • Manyvarieties incl. breadwheat, durum („pasta“) wheat… • Third most-producedcerealwith 651 millionstons (2010), cultivatedworldwide in different climates • Leadingsourceofvegetableprotein in human food

  3. The Challenge

  4. Wheat – a WGS approachAimsand Goals

  5. Wheat – a WGS approach • 5x 454 WGS sequencing => 85 Gbsequence, 220 millionreads • ~79% ofreadsrepeat-related • direct Low-copy-numbergenomeassembly (LCG, Newbler) => collapsesmanyhomologousgenesequences • topreventcollapsingofhomologousgenesequencesandreducecomplexity => orthologousgroupassemblyat high stringency

  6. WGS assembly using „in silico exon capture“ • Usefullysequencedandanalysedreferencegenomes (rice, Brachypodium, sorghum) • Group genes intofamilies (Orthologous Groups) • Usetheorthologousgrouprepresentativesassequencebaitstocapturecorrespondingsequencereads. • Do sub-assemblyforeach „orthologous bin“seperately

  7. BreadWheatGenaology

  8. Ortholomedirectedassemblycircumventslimitationsfacedby WGS assembly

  9. The ortholomedirectedassemblydeliversorderedsegments

  10. The ortholomedirectedassemblydeliversorderedsegments II 1 2 3

  11. Gene Copy Retention after Polyploidization - Calibrationofthemethod- Maize 97% 99% 100% Hexaploid Rice „TRice“

  12. Gene Copy Retention after Polyploidization

  13. Gene Copy Retention after Polyploidization

  14. ExpandedWheat Gene Families

  15. The Three Nephews: the A, B and D‘s of wheat Shotguns (Illumina 80x (T.monococcum)) and 454 (3x (Ae.tauschii)) cDNA seq‘s from the Ae. speltoides group (B) Can A and D genome shotgun data be used to dissect the ABD of wheat?

  16. The ThreeNephews: Similarity on a SequenceBasis

  17. Wheat A, B and D AssignmentusingMachine Learning (SVM)

  18. Particular Gene Categoriesarepreferentiallyretained

  19. Summary Almostfullgenecomplementdetectedandstructured 10000s of pseudogenes detected Separation of A, B and D usingmachinelearningwith > 75% accuracy Complementarytochromosomesortingapproaches Applicabletopolyploids in generaltogetgenomeoverview Rapid andeconomicapproachtopragmaticallycopewithlimitations in sequencetechnology Franz Marc „Hocken im Schnee“

  20. acknowledgements The UK WheatConsortium Mike Bevan Neil Hall Anthony Hall Keith Edwards Rachel Brenchley CSHL Dick McCombie UC Davis & USDA Albany Jan Dvorak Mincheng Luo Olin Anderson Kansas State University Bikram Gill Sunish Segal MIPS Matthias Pfeifer Klaus Mayer All othergroupmembers EBI Paul Kersey Dan Bolser

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