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.
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