User friendly tools for the Arabidopsis thaliana 1001 Genomes
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Introduction to a user friendly interface for the Arabidopsis thaliana 1001 Genomes.
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User friendly tools for the Arabidopsis thaliana 1001 Genomes
- 1. User-friendly web tools for the Arabidopsis thaliana 1001 genomes Beth Rowan Max Planck Institute for Developmental Biology Plant and Animal Genomes XXIV January 11, 2016
- 2. Why sequence 1001 Arabidopsis thaliana genomes? Brief history of variant discovery
- 3. Why sequence 1001 Arabidopsis thaliana genomes? Brief history of variant discovery SNPs 107 105 103 1995 2000 2005 2010 2015 First reference genome
- 4. Why sequence 1001 Arabidopsis thaliana genomes? Brief history of variant discovery SNPs 107 105 103 1995 2000 2005 2010 2015 First reference genome Haplotype map with 20 strains
- 5. Why sequence 1001 Arabidopsis thaliana genomes? Brief history of variant discovery SNPs 107 105 103 1995 2000 2005 2010 2015 First reference genome Haplotype map with 20 strains 2 wild strains resequenced
- 6. Why sequence 1001 Arabidopsis thaliana genomes? Goals -understand genome variation in the species -reconstruct demographic history -identify geographic and genetic subsets -generate a powerful resource for genome-wide association studies Brief history of variant discovery SNPs 107 105 103 1995 2000 2005 2010 2015 First reference genome Haplotype map with 20 strains 2 wild strains resequenced
- 7. Why sequence 1001 Arabidopsis thaliana genomes? Goals -understand genome variation in the species -reconstruct demographic history -identify geographic and genetic subsets -generate a powerful resource for genome-wide association studies Brief history of variant discovery SNPs 107 105 103 1995 2000 2005 2010 2015 First reference genome Haplotype map with 20 strains 2 wild strains resequenced >80 wild strains resequenced
- 8. Why sequence 1001 Arabidopsis thaliana genomes? Goals -understand genome variation in the species -reconstruct demographic history -identify geographic and genetic subsets -generate a powerful resource for genome-wide association studies Brief history of variant discovery SNPs 107 105 103 1995 2000 2005 2010 2015 First reference genome Haplotype map with 20 strains 2 wild strains resequenced >80 wild strains resequenced 1135 wild strains resequenced
- 9. 1001 Arabidopsis genomes: an overview 1001 Genomes Consortium, in review Final Set: 1135 Accessions
- 10. 1001 Arabidopsis genomes: an overview 1001 Genomes Consortium, in review Final Set: 1135 Accessions
- 11. 1001 Arabidopsis genomes: an overview 1001 Genomes Consortium, in review
- 12. 1001 Arabidopsis genomes: an overview 1001 Genomes Consortium, in review Nearly-identical pairs North America & British Isles
- 13. 1001 Arabidopsis genomes: an overview 1001 Genomes Consortium, in review Highly divergent pairs 26 “relict” accessions -Iberian peninsula -Cape Verde & Canary Islands Nearly-identical pairs North America & British Isles
- 14. 1001 Arabidopsis genomes: an overview ADMIXTURE analysis identifies 9 genetic groups 1001 Genomes Consortium, in review
- 15. 1001 Arabidopsis genomes web tools Current tools http://1001genomes.org/tools/ -easyGWAS -GWAPP -1001 Proteomes -GBrowse -POLYMORPH -BLAST -Alivie -TAIR converter -Col-0 DB New tools http://tools.1001genomes. org/ -Admixture map -Pseudogenomes -Strain ID
- 17. Admixture map
- 18. Admixture map
- 19. Admixture map
- 21. Pseudogenomes Select all Filter on the fly
- 25. Strain ID
- 27. Strain ID
- 28. Strain ID
- 29. Strain ID
- 30. Integrating tools with Araport JBrowse Extend to full dataset Variant tracks for each strain (Geographic location for each strain)
- 31. Integrating tools with Araport JBrowse Hover over variant to get info
- 32. Integrating tools with Araport JBrowse Left click on variant to see annotation and accession information
- 33. Integrating tools with Araport Future plans 1. Get all SNPs in region 2. Get all indels in region 3. Get SnpEff info for given SNP 4. Get VCF subset for given region 5. Get pseudogenomes 6. Helper function: Translate gene id to coordinates 7. Get allele frequencies for variants 8. Identify allele/haplotype groups 9. Find ADMIXTURE cluster membership 10. Experimental design tool for subsetting 1001 collection examples: -subset with greates genetic diversity -accessions with similar climates but from different geographical areas -accessions with different population histories
- 34. Integrating tools with Araport Future plans 1. Get all SNPs in region 2. Get all indels in region 3. Get SnpEff info for given SNP 4. Get VCF subset for given region 5. Get pseudogenomes 6. Helper function: Translate gene id to coordinates 7. Get allele frequencies for variants 8. Identify allele/haplotype groups 9. Find ADMIXTURE cluster membership 10. Experimental design tool for subsetting 1001 collection examples: -subset with greates genetic diversity -accessions with similar climates but from different geographical areas -accessions with different population histories https://www.surveymonkey.com/r/8DTCVQF
- 35. Acknowledgements Joffrey Fitz 1001 Genomes Consortium1001 Genomes Consortium Web ToolsWeb Tools Project coordinators Detlef Weigel Magnus Nordborg MPI for Developmental Biology Gregor Mendel Institute Joy Bergelson, University of Chicago Joe R. Ecker, Salk Institute Mitchell Sudkamp, Monsanto Database creation Congmao Wang, Zhejiang Acad. of Agri. Sciences Alexander Platzer, Gregor Mendel Institute +All Consortium Contributors Ümit Seren