TreeGenes: Enabling Visualization and Analysis in Forest Tree Genomics

Successfully identifying genes and alleles associated with traits of interest in forest trees requires robust integration of genotype, phenotype, and environmental data. Feasibility of these association studies depends on next-generation sequence data, ontologically sound phenotypes, and geo-referenced measures. The TreeGenes 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. We will discuss tools available through TreeGenes to access data from over 1700 forest tree species.

The TreeGenes database is designed to store and integrate data from public repositories as well as information that is not typically curated or submitted. In specific, we are actively collecting and curating metadata resulting from genotype:phenotype and genotype:environment association studies. The database is accessible through a variety of interfaces that deliver taxonomy views, literature searches, transcriptome annotations, genetic  maps (CMap), genome browsers (Gbrowse), and variant annotations.

TreeGenes hosts custom-developed tools that allow users to: track and manage high-throughput projects through the Forest Tree Genetic Stock Center, query and download bulk datasets through DiversiTree, and perform analysis of data on HPC resources using CartograTree. The upcoming transition to the more standardized Tripal database solution  will allow TreeGenes to integrate with other valuable repositories, including the Hardwood Genomics Web and the Genome Database for Rosaceae. The in-development Tripal Galaxy module will allow TreeGenes to offer an expanded set of analytical tools and flexible computing resources to users.