Bioinformatic Solutions in Forest Genomics: Accessing the TreeGenes Database

The Dendrome project provides custom informatics tools and databases to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is further enhanced with systems that are well connected with federated databases, automated data flows, machine learning analysis, standardized annotations and quality control processes. A sample tracking system 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. The supporting TreeGenes database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. Annotated transcriptomic studies resulting from next-generation sequencing are now available for several forest tree species, which includes visualization of the assemblies in GMOD’s GBrowse interface. 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.  Recent development has focused on web services to connect geo-referenced individuals with important ecological and trait databases in the form of a new utility known as CartograTree.  The combined resources of the Dendrome project serve as a powerful knowledge environment for genotype-phenotype information resulting from large-scale genomics projects.