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Icon 05 TreeGenes

Sequence Resources

Summary by Genus

Colleague Directory

Colleagues Organizations

Species Database

Forest Trees

Literature Database

Search Literature

Transcriptome Database

Search Transcriptome Transcriptome Summary

Protein Database

Search Proteins Protein Summary

Expression Studies

Search Expression Expr. Studies Summary

Association PopGen

View TGDR

DiversiTree

Genotype, Phenotype & Sequence CartograTree

Comparative Mapping Database

Published Maps Maps Recently Submitted Search Cmap

Genome Transcriptome Browser

Browser Portal

Submissions

Submit to TreeGenes

Icon 02 Links

Conifer Genome Network PineRefSeq Project SMarTForests Project Conifer Translational Genomics Network TreeGenes Database Dendrome Plone Forestry Careers and Education Resource

TreeGenes :: Overview

The TreeGenes database and Dendrome project provide custom informatics tools to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is enhanced with systems that are well connected with federated databases, automated data flows, machine learning analysis, standardized annotations and quality control processes. The database itself contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. GMOD GUI tools such as CMAP for genetic maps and GBrowse for genome and transcriptome assemblies are implemented here. A sample tracking system, known as the Forest Tree Genetic Stock Center, sits at the forefront of most large-scale projects. Barcode identifiers assigned to the trees during sample collection are maintained in the database to identify an individual through DNA extraction, resequencing, genotyping and phenotyping.

TreeGenes Schema

DiversiTree, a user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of resequencing data. It provides the community with access to data types describing individual tree samples including ESTs, primer sequences, SNPs, genotypes and phenotypes. The variety of outputs available allows users to perform high-resolution dissection of traits and relate molecular diversity to functional variation. CartograTree combines geo-referenced individuals with relevant ecological and trait databases in a user-friendly map-based interface.

A full summary of our current genomic resources by genus and species can be found here.

TreeGenes is housed in a PostgreSQL 9.0.10 database that is fed validated information from a variety of internal and external data sources (including NCBI, Gene Ontology, Plant Ontology, Pfam, TryDB, ExPASy, Ameriflux, WorldClim, and others). This information is presented to the research community through a web-based graphical interface environment. Data submission is critical to the value of this resource.

How to Reference TreeGenes:
Wegrzyn J.L., Lee J.M., Tearse B.R., and Neale D.B.,
"TreeGenes: A Forest Tree Genome Database",
International Journal of Plant Genomics, vol. 2008, Article ID 412875,
7 pages, 2008. doi:10.1155/2008/412875

Wegrzyn J.L., Main D., Figueroa B., Choi M., Yu J., Neale D.B., Stanton M., Zheng P., Ficklin S., Cho I., Peace C., Evans K., Volk G., Oraguzie N., Chen C., Jr. F.G., Abbott A.G.,
"Uniform standards for genome databases in forest and fruit trees",
Tree Genetics & Genomes, vol. 8, issue 3,
8 pages, 2011. doi:10.1007/s11295-012-0494-7

Icon 03 Updates

PineRefSeq project releases assembly (v1.01) of the Pinus teada genome CartograTree (v2.0.0) , a map interface that works with DiversiTree to bring together genomics, ecological, and trait data is now live! CartograTree (v3.0.0) Beta is available for testing. SMarTForests Project releases the third assembly of the Picea glauca genome

Icon 01 Events

2014 IUFRO Forest Tree Breeding Conference

Prague, Czech Republic
August 25-29, 2014
IUFRO Working Party International Conference

Vitoria-Gasteiz, Spain
September 9-12, 2014
Ecological & Evolutionary Genomics at the Gordon Research Conference

University of New England, Biddeford, ME
July 14-19, 2013

Icon 04 Contact

tg-help@ucdavis.edu

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