Bioinformatics resources for IITA Crops

Bioinformatics resources for IITA

Crops

GO Workshop3-6 August 2010

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

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

CHICK_OLF6

DNA annotation

Protein annotation

Data from Ensembl Genome browser

TRAF 1, 2 and 3 TRAF 1 and 2

Structural annotation:

catenin

Functional annotation:

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

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

http://www.plantgdb.org/

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

http://www.gramene.org/

http://www.gramene.org/

IITA Crops Global: Cowpea, Soybean, Bananas,

Plantain, and Yams Sub-Saharan Africa: Cassava and Maize

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?

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

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

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

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

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?

Yams

55577 Dioscorea rotundata white yam55571 Dioscorea alata water yam29710 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

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

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/

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?

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