1. Why do we need good quality annotations? Pankaj Jaiswal Oregon State University Gene Annotation Workshop July 31, 2010 ASPB Plant Biology 2010 Montreal, Canada

2. 2 Physical and/or Sequence map Map-2 Polymorphism Candidate gene Gene models Transcripts Peptides Function Expression Pathway Homologs Paralogs Orthologs Interactions Comparative and Translational Genomics Genetic markers & phenotypes (genes and QTL) Map-1 Forward Reverse Genotype Phenotype

3. Jaiswal lab: Strawberry Genome Consortium Schnable et al., pp. 1112 – 1115 (Maize synteny and Venn diagram) Comparative Genomics

4. Expression pattern and over-represented metabolic processes of rice diurnally cycling genes 0 4 8 12 16 20 24 28 32 36 40 44 48 -500 0 500 Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

5. Trp pathway genes-Diurnal expression pattern clustering 0 4 8 12 16 20 24 28 32 36 40 44 48 Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

6. Diurnal variation of Trp biosynthetic gene expression 0 4 8 12 16 20 24 28 32 36 40 44 48 0 hrs12 hrs24 hrs -200 0 200 Expression data provided by Todd Mockler, Analysis by Palitha Dharmawardhana (jaiswal lab)

7. Over-represented gene ontology categories associated to genes expressed in (A) Fruit and (B) Root. The circles are shaded based on significance level (yellow = FDR below 0.05), and the radius of each circle denotes the number of genes in each category. GO enrichment: RootGO enrichment: Fruit Data provided by Todd Mockler and Kevin Folta

8. 8 InterPro Uniprot & RefSeq MetaCyc Function Function Gene Ontology Genes EC number Text Mining Phenotype KEGG-Rice Gene-Pathway Expression Manual Curation Interactions Pathways Enriched Gene Function MonocotsDicots Orthologs (Compara/Inparanoid) Arabidopsis and OthersMaize, Rice and Others Non plants Genome/maps A3 B1 B2 C A1 A2 F B3 D A B C D

9. Annotations by homology !

10. Comparison of Metabolic Pathway Gene Annotations

11. 11 Race to the ……. ! Are we there yet ?

12. Solutions ! Get involved in the community curation Provide details as much as possible in your publications Work with your species specififc database (if available*) before/after publication on making sure data from your publication is integrated. – * If not available contact archives, succh as NCBI, Uniprot, Gramene. You need it, I need it, community needs it.