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Comprehensive Bioinformatics Resources for IITA Crops Genomic Annotation Workshop

This workshop focuses on genome annotation for IITA crops, including cowpea, soybean, bananas, plantains, and yams. Learn about structural and functional annotation processes, model organism databases, and sequencing consortia. Explore resources for various crops like cowpea, banana, and cassava, and understand the importance of genomic annotation for functional genomics and genetic improvement.

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Comprehensive Bioinformatics Resources for IITA Crops Genomic Annotation Workshop

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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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