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Integrating Genome and Transcriptome Resources into TreeGenes

Integrating Genome and Transcriptome Resources into TreeGenes. Jill Wegrzyn David Neale Doreen Main Keithanne Mockaitis. University of California at Davis Washington State University Indiana University/Center for Genomics and Bioinformatics.

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Integrating Genome and Transcriptome Resources into TreeGenes

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  1. Integrating Genome and Transcriptome Resources into TreeGenes Jill Wegrzyn David Neale Doreen Main KeithanneMockaitis University of California at Davis Washington State University Indiana University/Center for Genomics and Bioinformatics

  2. TreeGenes DatabaseEncompasses Dendrome Resources, DendromePlone, TreeGenes Database &DiversiTree • Ten modules to store and interrelate data for query and analysis in PostgreSQL • Direct resource for nearly 2,500 forest geneticists representing 800 organizations worldwide. Over 6,000 unique visitors in December 2011. • Forest Geneticists Colleague module • Literature module • EST annotation pipeline and module • Comparative map module • Species module • Sequencing module • Primers module • Genotype/EST module • Phenotype/Expression module • Sample tracking module

  3. Genomic Resources 678 Species Representing 77 Genus

  4. CMAP: Obtaining TreeGenes (TG) Accession Number (optional) Add additional map files Obtain TG Accession number! Add literature data and (first) map file

  5. Individual features and their locations on map List of features on map

  6. GMOD Genome Browser Search and Select data source Tracks can be reordered or hidden as necessary

  7. Transcriptome Assembly Summary Loblolly pine 454 (JGI and CGB) Douglas-fir RNASeq (FS) and 454 (JGI) Sugar pine RNASeq (FS) and 454 (JGI)

  8. Douglas-fir Transcriptome Resources in TreeGenes

  9. Forest Tree Genetic Stock Center

  10. TreeGenes Sample Tracking System • Accurately track samples through collection, DNA extraction, and genotyping • Provide a standard and efficient method to collect and store phenotypic data • Provide a public interface to readily query raw genotype, phenotype, and association results (DiversiTree) • Provide interfaces and database backend to support a DNA distribution center (UCD)

  11. Data Submission Phenotype Data Forest Tree Genetic Stock Center Sample Submission Phenotypes Defined Accession Number Genotypes DiversiTree Raw Data Accession Number Literature Object Sequencing Centers

  12. Ontology Development Plant Ontology and Trait Ontology • Plant Ontology • Structure • Needle, Cambium • Growth stages • Trait Ontology • Forest Tree Specific Phenotypes • Wood Density • PATO • Phenotypic Qualities • Forest Tree Ontology Meeting (PO and TO) – Feb. 2012 • NSF Funded Plant Genome Research Resource

  13. Genomic resources

  14. Web Services Development Communication within TreeGenes • Development of Web Services in cooperation with NSF’s iPlantCyberinfrastructure Project • Software system to support interoperable machine to machine interaction over a network regardless of platform incompatabilities • Web service descriptive language (WSDL) is implemented to relate operations

  15. SSWAP Ontology Creating and Contributing to Existing Servlets for Common Genomic Types

  16. Bulk Retrieval Window Components Data & Annotation Selection Fields Bulk Retrieval Window

  17. GenSAS development with Content Management Plone and Drupal login/signup panel query sequence panel data retrieval panel tool selection panel task queue panel

  18. GenSAS development Multiple Gene Prediction Tracks overview track control track sequence track evidence tracks custom track function track message box

  19. GenSAS integration with Gbrowse Prototyped with Peach Genome in GDR

  20. Analysis Resources Custom Databases

  21. Integrating Tools into TreeGenes Galaxy

  22. Acknowledgements University of California at Davis Ben Figueroa John Liechty John Yu Hans Vasquez-Gross USFS Rich Cronn Jessica Wright Brian Knaus HardeepRai UGA Jeffrey Dean Walt Lorenz More Information C19 Monday, 1:50 pm P064

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