Gramene
- 2. Gramene • http://www.gramene.org/ • Curated, open-source, integrated data resource • Comparative functional genomics in crops and model plant species • Several platform infrastructures are linked • This work is a joint project between EnsemblGenomes (European Bioinformatics Institute) and the group of Doreen Ware at the Cold Spring Harbor Laboratory
- 3. • A resource for plant comparative genomics based on Ensembl technology. • Exploration of genome features, functional ontologies, variation data and comparative phylogenomics. • two main frameworks: genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). • Major funding: National Science Foundation, United States Department of Agriculture - Agricultural Research Service Gramene
- 5. Collaborators • Arabidopsis 1001 genomes • Arabidopsis Information Portal (AIP) • Banana genome • Beijing Genome Institute (BGI) • CIMMYT • Chinese Academy of Agriculture (Inst of Veg & Flowers) • DOE Joint Genome Institute (JGI) • Ensembl Genomes (EBI) • Gene Discovery in Cereals (Wheat) • Grape genome (CRIBI, IGGP) • ICRISAT • International Barley Sequencing Consortium (EBI collaboration) • Maize Diversity (Panzea) • Maize Expression • Maize genome (Wilson) • National Center for Biotechnology Information (NCBI) • Oryza genomes (OMAP & OGE) • Plant Metabolic Network • Rice Genome Annotation Project (RAP- DB) • Sorghum Diversity • UniProt • Wheat D genome project
- 6. Informations in Gramene • Fully assembled reference genomes • integrated using ontology-based annotation and comparative analyses • Additional community data, such as genetic variation, expression and methylation • The Plant Reactome pathway portal -reference resource for analyzing plant metabolic and regulatory pathways • provide previously reported resources on comparative maps, markers and QTL
- 7. Plant Genomes • The website, database and its contents continue to be updated five times per year • Changes can be followed at the Gramene news portal • All reference genome assemblies are accessioned with the International Nucleotide Sequence Database Collaboration NSDC (http://www.insdc.org)
- 8. Plant Genomes 44 entries 1806919 genes • Aegilops tauschii • Arabidopsis thaliana • Beta vulgars • Brassica napus • Glycine max • Hordeum vulagare • Oryza spp. • Populus trichocarpa • Prunus persica • Solanum lycopersicum • Solanum tuberosum • Sorghum bicolor • Theobroma cocoa • Triticum aestivum • Vitis venifera • Zea mays
- 9. ANNOTATION AND COMPARATIVE GENOMICS • A principal aim:Gramene is to integrate and draw connections between genomes through consistent functional annotation and comparative analyses • Protein-coding genes from all species were used to build phylogenetic gene trees using the Ensembl Compara Gene Trees pipeline
- 11. PLANT GENETIC DIVERSITY AND SEQUENCE VARIATION • Gramene provides SNP and/or structural variation data sets for 11 genomes • Eg: The new bread wheat variation data include over 1.5 million SNPs from the Wheat HapMap study
- 12. PLANT PATHWAYS • The pathway portal (http://www.gramene.org/pathways) provides resources for comparative analysis of plant pathways across several model and crop plant species • The Plant Reactome (http://plantreactome.gramene.org) a database of plant metabolic and regulatory pathways, was developed collaboratively by Gramene and the Human Reactome project • The Reactome data model – gene products, small molecules and macromolecular interactions into reactions and pathways to build a systems-level framework of an eukaryotic organism – to illustrate how it is influenced by intrinsic developmental cues and in response to various signals originating in the surrounding environment • The Plant Reactome features O. sativa as a reference species
- 13. PLANT PATHWAYS • The pathways are organized based on a hierarchical classification • The detailed view of a pathway shows a graphical display of the various associated reactions, enzymes, metabolites and cofactors in the context of their subcellular locations • Links are also provided to Gramene gene loci and several external resources like UniProt, PIR, ChEBI, PubChem, PubMed and GO
- 15. PLANT GENE EXPRESSION ATLAS • Collaboration with the EMBL-EBI's Expression Atlas (http://www.ebi.ac.uk/gxa) project • Information about gene expression assayed in samples of different cell types, organism parts, developmental stages, diseases and other conditions • data include microarray and RNA-sequencing studies
- 16. WEBINARS AND VIDEO-TUTORIALS • In November 2014 • began to offer monthly webinars • Focus on providing an overview of resources and functionalities available for comparative plant genomics • Explaining how users can visualize and analyze data of their choice using various built-in tools. • The recorded webinars are available on Gramene's YouTube channel (https://goo.gl/qQ2Pjn)