SAB presentation to Jim narrated

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Tecnologia

Ecological and evolutionary functional genomics: finding & studying genes that matter Christopher W. Wheat

Ecological and Evolutionary Functional Genomics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing C. Vera and C. Wheat, Fescemyer, Frilander, Crawford, Hanski, Marden 2008

First de novo transcriptome assembly using 454 pyrosequencing SNP’s

Annotation of 45,000 contigs + singletons Predicted genes: D. melanogaster = 13,379 B. mori = 18,510 Estimated coverage : 70% D. mel estimate 50% B. mori estimate Lower estimate 50% genes

Metabolic Map Comparison ,[object Object],Bombyx mori with WGS

Increasing 454 sequencing (Aland + China & France) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],Wheat et al., in prep. Population age: P = 0.02

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Mixed Model Analysis : popage & peak metabolic rate Popage fixed effects: dye popage bodymass popage*bodymass PMR fixed effect: dye PMR Random effects: slide array(slide) spot spot*array individual (FDR threshold = 5%) Using JMP Genomics (SAS)

Mixed model analysis of Abdomen ANOVA normalized (Multiple test correction used FDR @ 5% = 3.16 -log10P) ,[object Object],[object Object],-log 10 P-value

Significantly different genes (FDR threshold = 5%) Peak Metabolic Rate Continuous Wheat et al., in prep. 623 33 188 656 Population Age 221 Categorical

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Biological validation: vitellogenin ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Temperature treatments Last instar larvae Reared in lab Study gene expression Kvist et al., in prep. 20 o C 26 o C 35 o C Temperature maximum Cold Standard Hot Treatments Hot Standard Cold

Summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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SAB presentation to Jim narrated

1. Ecological and evolutionary functional genomics: finding & studying genes that matter Christopher W. Wheat

3. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing C. Vera and C. Wheat, Fescemyer, Frilander, Crawford, Hanski, Marden 2008

4. 48k contigs

5. First de novo transcriptome assembly using 454 pyrosequencing SNP’s

6. Annotation of 45,000 contigs + singletons Predicted genes: D. melanogaster = 13,379 B. mori = 18,510 Estimated coverage : 70% D. mel estimate 50% B. mori estimate Lower estimate 50% genes

7. Upper estimate of 70% = 13,142 genes

10.

11.

12.

13. Mixed Model Analysis : popage & peak metabolic rate Popage fixed effects: dye popage bodymass popage*bodymass PMR fixed effect: dye PMR Random effects: slide array(slide) spot spot*array individual (FDR threshold = 5%) Using JMP Genomics (SAS)

14.

15. Significantly different genes (FDR threshold = 5%) Peak Metabolic Rate Continuous Wheat et al., in prep. 623 33 188 656 Population Age 221 Categorical

16.

17.

18. Temperature treatments Last instar larvae Reared in lab Study gene expression Kvist et al., in prep. 20 o C 26 o C 35 o C Temperature maximum Cold Standard Hot Treatments Hot Standard Cold

19.

SAB presentation to Jim narrated

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