1 Comparative analyses of the Comparative analyses of the potato and tomato transcriptomes potato and tomato transcriptomes David Francis, Allen David Francis, Allen Van Deynze Van Deynze , John , John Hamilton, Walter De Jong, David Douches, Hamilton, Walter De Jong, David Douches, Sanwen Huang, and C. Sanwen Huang, and C. Robin Buell Robin Buell Supported by the AFRI Plant Breeding, Genetics, and Supported by the AFRI Plant Breeding, Genetics, and Genomics Program of USDA’s National Institute of Food Genomics Program of USDA’s National Institute of Food and Agriculture and Agriculture
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Comparative analyses of the potato and tomato transcriptomes
Comparative analyses of the potato and tomato transcriptomes. David Francis, Allen Van Deynze , John Hamilton, Walter De Jong, David Douches, Sanwen Huang, and C. Robin Buell. - PowerPoint PPT Presentation
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Comparative analyses of the potato Comparative analyses of the potato and tomato transcriptomesand tomato transcriptomes
David Francis, AllenDavid Francis, AllenVan DeynzeVan Deynze, John Hamilton, , John Hamilton, Walter De Jong, David Douches, Sanwen Huang, Walter De Jong, David Douches, Sanwen Huang, and C. and C. Robin BuellRobin Buell
Supported by the AFRI Plant Breeding, Genetics, and Supported by the AFRI Plant Breeding, Genetics, and Genomics Program of USDA’s National Institute of Food and Genomics Program of USDA’s National Institute of Food and
AgricultureAgriculture
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Questions
International Sol Project: How can a common set of genes/proteins give rise to such a wide range of morphologically and ecologically distinct organisms?
SolCAP: How can variation be harnessed to improve varieties that benefit the consumer, processors, and the environment?
Sequence data available to address these questions:
S. phureja draft genome sequence
S. tuberosum, S. lycopersicum, S. pimpinellifolium GAII transcriptomes
Technology
Next Generation Sequencing
SNP genotyping
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What comparisons do we want to make?
How well do S. tuberosum expressed sequences align to S. phureja genomic sequences?
How well do S. lycopersicum expressed sequences align to S. phureja genomic sequences?
How is variation distributed within a Species?
within a market class?
within a variety?
within a gene?
Which sequence variation is important to phenotypic variation?
Library creation/QC GAII sequencing (single and paired end)
Comparison of two genes on tomato chromosome 9 BAC
COSII
Fresh Market vs Fresh Market Identities = 573/573 (100%), Gaps = 0/573 (0%)Fresh Market vs Processing Identities = 569/569 (100%), Gaps = 0/569 (0%)S. lycopersicum vs S. pimpinellifolium Identities = 339/341 (99%), Gaps = 0/341 (0%)Potato vs Potato Identities = 606/612 (99%), Gaps = 0/612 (0%)Tomato vs Potato Identities = 914/948 (96%), Gaps = 6/948 (0%)
DIVERGED SEQUENCE
Fresh Market vs Fresh Market Identities = 959/959 (100%), Gaps = 0/959 (0%)Fresh Market vs Processing Identities=1560/1560(100%), Gaps=0/1560 (0%)S. lycopersicum vs S. pimpinellifolium Identities = 612/613 (99%), Gaps = 0/613 (0%)Tomato vs Potato Identities = 223/280 (79%), Gaps = 11/280 (3%)Potato vs Potato Identities = 246/278 (88%), Gaps = 7/278 (2%)
What patterns do we expect to see for genes “under selection”?•Low Variation (fixed)•High Ka/Ks (mutations affect protein, possible diversifying selection)•Mutations (loss of function)•FST (genes that distinguish populations)
All 173 markers (K=6)
89 Coding markers (K=5)
84 Non-coding markers (K=6)
Processing Fresh-market Vintage Landrace
500K burnin/750K MCMC reps, 20 runs for each K from 3 to 8