1. Whole Genome Sequencing &Crop Genetic Breeding Presentation: Wenhui Gao 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. Pseudochromosome construction (Qiang Xu et al. Nat Gen. 2013)

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

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

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 (Hovav et 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 Vitis vinifera & Theobroma cacao synteny 99.95%(761.4Mb) was anchored

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

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

28. Evolution of functional gene families CESA CSL MYBs NBS

29. CESA

30. CSL

31. MYB subgroup 9

32. NBS Gr Chromosome7 Tc Chromosome7 Gr Chromosome13

33. Genome Visualization

34. 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

35. 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

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

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

38. Homeolog loss and biased gene expession

39. 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)

40. (Chen J et al. Nature Communications. 2013)