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Bioinformatics resources for IITA Crops

Bioinformatics resources for IITA Crops. GO Workshop 3-6 August 2010. IITA Crops. Genome annotation General plant genome resources IITA crops What is needed?. Genomic Annotation.

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Bioinformatics resources for IITA Crops

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  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: • identifying functional elements in the genome: “structural annotation” • attaching biological information to these elements: “functional annotation” • biologists often use the term “annotation” when they are referring only to structural annotation

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

  5. Functional annotation: catenin

  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/

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

  10. http://www.gramene.org/

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

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

  13. 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?

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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?

  19. Yams 55577 Dioscorea rotundata white yam 55571 Dioscorea alata water yam 29710 Dioscorea 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

  20. 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

  21. 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/

  22. 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?

  23. 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

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