Growing and cultivating the forest genomics database, TreeGenes

Abstract

Forest trees are valued sources of pulp, timber and biofuels, and serve a role in carbon sequestration, biodiversity maintenance and watershed stability. Examining the relationships among genetic, phenotypic and environmental factors for these species provides insight on the areas of concern for breeders and researchers alike. The TreeGenes database is a web-based repository that is home to 1790 tree species and over 1500 registered users. The database provides a curated archive for high-throughput genomics, including reference genomes, transcriptomes, genetic maps and variant data. These resources are paired with extensive phenotypic information and environmental layers. TreeGenes recently migrated to Tripal, an integrated and open-source database schema and content management system. This migration enabled developments focused on data exchange, data transfer and improved analytical capacity, as well as providing TreeGenes the opportunity to communicate with the following partner databases: Hardwood Genomics Web, Genome Database for Rosaceae, and the Citrus Genome Database. Recent development in TreeGenes has focused on coordinating information for georeferenced accessions, including metadata acquisition and ontological frameworks, to improve integration across studies combining genetic, phenotypic and environmental data. This focus was paired with the development of tools to enable comparative genomics and data visualization. By combining advanced data importers, relevant metadata standards and integrated analytical frameworks, TreeGenes provides a platform for researchers to store, submit and analyze forest tree data.

Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment

“…TreeGenes remained in a custom database schema and website, adopting components of the Generic Model Organism (GMOD) framework for housing genetic maps (cMAP) and genome assemblies (JBrowse) (Stein et al, 2002). Later development focused on the integration of genotyping resources, phenotypes, expression studies, and additional reference genome sequences (Wegrzyn et al, 2012; Falk et al, 2018).…”

“…TreeGenes currently represents just over 1700 species from 16 orders and 124 genera (Falk et al, 2018). TreeGenes has 1200 registered users with associated colleague accounts that enable access to data submission and analytical pipelines.…”

ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

“…The unavailability of reference genome assemblies constrains the scope of genomic studies in non-model species, as is the case for the vast majority of woody plant species (Falk et al, 2018). In this context, the use of reduced representation genotyping methodologies, such as double-digested RAD sequencing (ddRADseq; Peterson et al, 2012), largely facilitates genomic analysis (Hirsch et al, 2014), and has been already used in the phylogenetic analysis (Hipp et al, 2020) and genetic mapping of oak species (Konar et al, 2017).…”

TOA: A software package for automated functional annotation in non‐model plant species

“…All gene sets in Phytozome are annotated with KOG, KEGG and the InterPro family of protein analysis tools. TreeGenes (Falk et al., 2018; Wegrzyn et al., 2008, 2012) is a database that provides genome‐wide data, transcriptomes (cDNA, EST and TSA) and unigenes for a small number of the 2,026 species of forest trees included in the database. Treegenes provides also a web interface to perform homology searches against genomic and transcriptomic sequences derived from next generation sequencing.…”