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