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Whole Genome Sequencing &Crop Genetic Breeding

Whole Genome Sequencing &Crop Genetic Breeding. Presentation: Wenhui Gao E-mail: gaowenhui2012@gmail.com. Compeleted genomes in 2013. Outline. 1. Introduction to s equencing technology 2. Process of genome sequencing analysis 3 . Comprehensive comparison  of two cotton genomes

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Whole Genome Sequencing &Crop Genetic Breeding

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  1. Whole Genome Sequencing &Crop Genetic Breeding Presentation: WenhuiGao E-mail: gaowenhui2012@gmail.com

  2. Compeleted genomes in 2013

  3. Outline 1. Introduction to sequencing technology 2. Process of genome sequencing analysis 3. Comprehensive comparison of two cotton genomes 4. Prospect and challenge of genome sequencing

  4. 1. Introduction to sequencing technology (Wendy et al. Molecular Systems Biology. 2013)

  5. Development of sequencing technology

  6. 2. Process of genome sequencing analysis • DNA Isolation & Library construction • Sequencing, assembly, BAC Assessment& anchoring to chromosome • Repeat sequences mask and annotation • Gene prediction & annotation • Comparative genome & evolution analysis • Species-specific biology analysis • Genome visualization and data submission

  7. Two strategies for Whole Genome Sequencing

  8. Genome assembly

  9. Assessment of assembly accuracy (The Potato Genome Sequencing Consortium. Nature. 2011)

  10. Pseudochromosomeconstruction (QiangXuet al. Nat Gen. 2013)

  11. Gene prediction & annotation • Prediction • De novo prediction • Homology-based prediction • Transcript-based prediction • Annotation • Pfam • KEGG • Gene Ontogy • InterPro • Model organism (The Tomato Genome Consortium. Nature. 2012) (QiangXuet al. Nat Gen. 2013)

  12. Comparative genome & evolution analysis Comparative genome Phylogenetic tree Whole Genome Duplicate (Kunbo Wang et al. Nat Gen. 2012) (Vladimir Shulaevet al. Nat Gen. 2010) (Jeremy Schmutz et al. Nature. 2013)

  13. Species-specific biology analysis • Take more attention on the important traits • Analysis Metabolic pathway • Gene family • Gene expression patterns • Copy Number Variation

  14. Genome visualization and data submission

  15. 3. Comprehensive comparison of two draft genomes of cotton (Kunbo Wang et al. Nat Gen. 2012) (Paterson et al. Nature. 2013)

  16. Introduction to cotton (Hovavet al., PNAS, 2008)

  17. Library preparation

  18. Cotton genome assembly

  19. Assessment of sequence assembly

  20. Anchor to chromosome 1369 Markers totally 43.8% of the markers (599) were unambiguously located on the assembly 73.2%(567.2Mb) was anchored 2800 +262 Markers and Vitisvinifera& Theobroma cacao synteny 99.95%(761.4Mb) was anchored

  21. Repeat mask and annotation Retrotransposons(LTRs): 42.6% DNA-transposons: 4.4% Other repeat: 13% Total: 60% Retrotransposons: 53% DNA-transposons: 1.5% Satellite tandem: <1% Total: ~56%

  22. Gene prediction and annotation 40,976 protein-coding genes 37,505 protein-coding genes 77,267 transcripts

  23. Comparative genome & evolution analysis

  24. Biology Stories In the paper of Paterson, there was a few work about the biology related problems. The main point of this paper was to discuss the evolution about cotton from the whole genome and gene family level.

  25. The evolution in Gossypium • Evolution from Gr Whole Genome level • Evolution from specific gene families level

  26. Evolution from Gr Whole Genome

  27. Evolution of functional gene families • CESA • CSL • MYBs • NBS

  28. CESA

  29. CSL

  30. MYB subgroup 9

  31. NBS Gr Chromosome13 Gr Chromosome7 Tc Chromosome7

  32. Genome Visualization

  33. Conclusions about two cotton genomes • Similar process in half part of genome analysis • Different genome sequencing strategies • Library preparation and sequencing platforms • Different effect in the final genome • The integrity and accuracy of genome • Different main points in two papers • China: Whole Genome Duplicate and biology stories • USA : Genome Evolution

  34. Prospect and Challenge of Genome Sequencing • Need do more work in future WGS • Problems in assembly and alignment (Short reads) • Trends in plant genome sequencing • Research in polyploidy genome (Homology) • Assembly and alignment • Anchor(Just Using simple Markers is not enough) • Homologous gene biased expression

  35. Third-generation DNA-sequencing technologies (John Eid et al. Science. 2009)

  36. Plant genome sequencing (Catherine et al. Trends in Plant Science. 2011)

  37. Homeolog loss and biased gene expession

  38. Personal viewpoint about Whole Genome Sequencing • Each step is important in the process of whole genome sequencing • Make the most of the genome sequencing resource (Not just for one paper) • The time of polyploidy genome sequencing is coming (challenge and opportunity coexist)

  39. Thank you (Chen J et al. Nature Communications. 2013)

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