Gramene

Gramene is a resource for plant comparative genomics based on Ensembl technology. It includes exploration of genome features, functional ontologies, variation data and comparative phylogenomics. Two main frameworks are included in genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases).

1. GRAMENE By, Bhavyasree R K PhD Genetics & Plant Breeding

2. Gramene http://www.gramene.org/ Curated ,  open-source ,  integrated  data resource C omparative 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

4. GRAMENE PORTAL

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

10. 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

11. 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

12. 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

13. 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 

14. 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 )

15. THANK YOU…….