1. Tomato genome annotation/ transcriptomics workshop Rome, March 17-19, 2010 Main Conclusions

2. Participants: Stephane Rombauts, Univ of Ghent Ioannis Filippis, Imperial College Asis Hallab, MPIZ Manuel Spannagl, MIPS Heidrun Gundlach, MIPS Zhangjun Fei, Boyce Thompson Institute Mohammed Zouine, Univ of Toulouse Fabio Fuligni, Univ di Milano Arnaud Bovy, Univ. ofWageningen R Klein Lankhorst, Univ. of Wageningen Roeland van Ham, Univ. of Wageningen Erwin Datema, Univ of Wageningen Maria Luisa Chiusano, Univ di Napoli Walter Sanseverino, Univ di Napoli Nunzio D'Agostino, Univ. di Napoli Alessandra Traini, Univ. di Napoli Miriam di Filippo, Univ. di Napoli Mara Ercolano, Univ. di Napoli Marco Pietrella, ENEA Gianfranco Diretto, ENEA Giovanni Giuliano, ENEA

3. Conclusions, Annotation Annotation is good enough for gene family/pathway captains to start manual annotation now. All data will revolve around iTAG annotation-Suynchronization of SGN, MIPS and CAB essential Only tweaking will be needed to adapt main conclusions to final annotation Manual annotation will be both hypothesis-driven and data-driven. Hypothesis-driven: Gene families/pathways important for tomato biology (carotenoid genes, ethylene receptors, etc) Data-driven: Focus will be on genes-gene families showing: Unexpected expansion/reduction Fruit-specific expression Specific to tomato (by OrthoMCL) Annotation jamboree will be organized on an island after paper submission

4. Conclusions, Transcriptomics Illumina and 454 RNAseq data are being aligned on genome. Gene models supported by Illumina data have been provided to Affy for chip design Protocol has been worked out for polishing 454 data before submission Evidence for alternative splicing Inclusion of tissue-specific RNAseq data is important for biological conclusions on the paper Cluster of companion papers under production Inclusion of peptide data on Gbrowse is important and innovative

5. Task division Blast Arabidopsis proteins significantly longer from tomato ones to scaffolds: Rombauts Study genome duplication: Rombauts (Paterson) Building pseudomolecules, physical mapping: Sato, Arizona, Keygene Feed peudomolecules to assembly, assembly correction: van Ham Chromosome heatmaps/Repetitive element annotation/ FISH pictures: Chiusano, Gundlachs, De Jong OrthoMCL clusters: Spannagl Human Readable Descriptions, Dendrograms: Allab Enrichment analysis: Not assigned Collection of RNAseq data: Giuliano Alignment of 454, Illumina and SOLID data: Filippis, Rombauts, Alioto Generation of alternative splicing annotation: Rombauts, Fei Inclusion of peptide data on genome browser: Zouine, SGN, MIPS Inclusion of BAC ends on genome browser: Datema Align old array probes on genome annotation: Fei

6. Data-driven manual annotation Look for expanded-contracted orthoMCL groups. Look for tomato-specific orthoMCL groups. Verify if they are supported by expression data Look for fruit-expressed genes Identify appropriate gene family/pathway captains

7. Hypothesis-driven manual annotation Gene family/pathway captains: Ethylene biosynthesis/Signal transduction: Giovannoni ARFs: Bouzayen Carotenoid biosynthesis, photomorphogenesis: Giuliano Ascorbate: Botella Transcription factors: Chiusano, Fei,Khurana R genes: Ercolano, others? Cyt p450s: Bishop Repeats: Gundlach miRNA prediction: Rombauts

8. Manual annotation details Informations that will be provided to gene family/pathway captains: Access to Gbrowse Table w automated iTAG annotation, including human readable gene descriptions Scaffold information OrthoMCL cluster information (tomato-Arabidopsis-rice-grape), including dendrograms Gene expression, including tissue-specific data Informations they will have to provide: Biological story, including interesting mutants, w focus on fruit biology. Synteny and gene duplication history using OrthoMCL and dendrogram information Input phenotypic data/gene name/protein name on table and on Bogas webpage Pathway picture in Pathvisio format Dendrogram of the protein family, in standard format Expression heatmap in standard format