TreeGenes and CartograTree: Tools for Forest Tree Genomics

Successfully identifying the genes and alleles associated with traits of interest in forest trees is dependent on access to genotype, phenotype, and environmental data. The future of these association studies lies in next-generation sequence data, ontologically sound phenotypes, and geo-referenced measures. 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. We will discuss tools available through the Dendrome project including the TreeGenes database, the DiversiTree interface, and the CartograTree tool which links phenotypic, genotypic, and environmental data in a geo-referenced application. TreeGenes is a database resource that provides tools to track, analyze, and collect data. In addition to connecting to external databases, TreeGenes is designed to integrate data that is otherwise not recorded by other available resources such as genotype:phenotype and genotype:environment studies. TreeGenes provides a variety of ways to view and filter data, and includes literature searches and comparative map displays.  The database enables users to access this information, as well as genome assemblies, with GMOD project tools such as Gbrowse and CMAP. DiversiTree allows users to search phenotype, genotype, and sequence data. The map-based CartograTree interface combines this information with environmental metrics from sources such as Ameriflux and WorldClim.  These connections are enabled via web services as implemented in SSWAP (Simple Semantic Web Architecture and Protocol) and allow researchers to directly access HPC resources to analyze their data with software such as MUSCLE and TASSEL.