1. Bioinformatics resources for IITA Crops GO Workshop 3-6 August 2010

2. IITA Crops  Genome annotation  General plant genome resources  IITA crops  What is needed?

3. Genomic Annotation  Genome annotation is the process of attaching biological information to genomic sequences. It consists of two main steps: 1. identifying functional elements in the genome: “structural annotation” 2. attaching biological information to these elements: “functional annotation”  biologists often use the term “annotation” when they are referring only to structural annotation

4. CHICK_OLF6 DNA annotation Protein annotation Data from Ensembl Genome browser TRAF 1, 2 and 3TRAF 1 and 2 Structural annotation:

5. catenin Functional annotation:

6. Bioinformatics Resources  Model Organism Databases (MODs) & Sequencing Consortia – organise and control genome annotation  NCBI – public sequence resources (collate, annotate, analysis)  UniProt – functional annotation (also displays GO)  Functional genomics tools – e.g. arrays  GO Consortium – members supply GO annotations to support functional modeling

7. http://plants.ensembl.org/index.html

8. http://www.plantgdb.org/

10. http://virtualplant.bio.nyu.edu/cgi-bin/vpweb2/virtualplant.cgi

11. http://www.gramene.org/

13. IITA Crops  Global: Cowpea, Soybean, Bananas, Plantain, and Yams  Sub-Saharan Africa: Cassava and Maize

14. Cowpea  Vigna unguiculata (taxon:3917) & subspecies  JCVI – “reduced representation” sequencing (clone ends) of Blackeye 5  54,123 genome sequences  187,483 ESTs  Annotated via homology to Arabidopsis & other plants  GO annotation via homology – availability?

15. Cowpea  Vigna unguiculata (cowpea) has 1,510 GO annotations for 175 proteins  Vigna unguiculata subsp. unguiculata (cowpea) has 25 annotations for 5 proteins  University of Cape Town Cowpea 9K drought stress SSH library  some studies using soybean microarray

16. Soybean  Glycine max (taxon:3847)  genome sequencing at DOE JGI as a preliminary assembly  NCBI: 1,459,639 ESTs, 34,946 proteins, 2,882 genes  UniProt: 12,837 proteins (EBI GOA automatic GO annotation)  UniGene assemblies available  multiple microarrays available

19. Banana  Musa acuminata (taxon:4641) & subspecies  Global Musa Genomics Consortium (GMGC) - in progress (includes JCVI, NARO)  7,102 genome sequences  14,864 ESTs  1,399 NCBI proteins; 680 UniProt

20. Banana  Musa acuminata (sweet banana): 3898 GO annotations to 491 proteins  Musa acuminata AAA Group (Cavendish banana): 579 annotations to 96 proteins  SAGE libraries generated for Musa acuminata

21. Plantain  Musa ABB Group (taxon:214693) - cooking banana or plantain  11,070 ESTs, 112 proteins  173 GO annotations to 53 proteins  functional genomics based on banana?

22. Yams 55577Dioscorea rotundata white yam 55571Dioscorea alata water yam 29710Dioscorea cayenensis yellow yam  Dioscorea (taxon:4672) & subspecies  NCBI: 31 ESTs, 623 proteins  Genome sequencing for Dioscorea alata – EST development (IITA & VSU)  183 GO annotations to 25 proteins

23. Cassava  Manihot esculenta (taxon:3983)  ESTs: 80,631  EST projects at Centre National de la Recherche Scientifique & University of Illinois at Urbana- Champaign  Genome sequencing in progress at DOE JGI  NCBI proteins: 568, UniProt:253  2,251 GO annotations assigned to 218 proteins  2 Euphorbia esula (leafy spurge) /cassava arrays

24. Maize  Zea mays (taxon:4577)  Genome sequencing completed by Washington University – other subspecies being sequenced  Active GO annotation project - 131,925 GO annotations to 20,288 proteins http://www.gramene.org/

28. IITA Crops: what is needed  Do we really need a MOD for every species?  How do we co-ordinate genome updates/structural annotation?  Functional annotation to support functional genomics (arrays, RNA-Seq, proteomics)?  Nomenclature to support comparative genomics?  Functional modeling of disease/infection?  Genetic makers for improvement – do we need to understand molecular mechanisms?  How can we leverage existing resources?

29. AgBase Collaborative Model  How can we help you?  Can make GO annotations public via the GO Consortium  Have computational pipelines to do rapid, first pass GO annotation (including transcript/EST sequences)  Provide bioinformatics support for collaborators  Developing new tools  Training/support for modeling data