1 / 20

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 …

lael-potts
Télécharger la présentation

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

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related