Growing and cultivating the forest genomics database, TreeGenes.

Area of Science:

• Forestry science
• Genomics
• Bioinformatics

Background:

• Forest trees are vital for timber, biofuels, carbon sequestration, and biodiversity.
• Understanding genetic, phenotypic, and environmental factors is crucial for tree breeding and research.
• The TreeGenes database serves as a repository for tree genomic and phenotypic data.

Purpose of the Study:

• To describe the recent developments and enhanced capabilities of the TreeGenes database.
• To highlight the integration of genetic, phenotypic, and environmental data for forest trees.
• To showcase the platform's utility for researchers in data storage, analysis, and visualization.

Main Methods:

• Migration of the TreeGenes database to the Tripal open-source system.
• Integration of high-throughput genomics data (genomes, transcriptomes, genetic maps, variant data) with phenotypic and environmental data.
• Development of tools for georeferenced accessions, metadata acquisition, ontological frameworks, comparative genomics, and data visualization.

Main Results:

• The TreeGenes database now hosts 1790 tree species and over 1500 users.
• Enhanced data exchange and analytical capacity through Tripal migration and partner database integration (Hardwood Genomics Web, Genome Database for Rosaceae, Citrus Genome Database).
• Improved integration of multi-omics and environmental data through coordinated georeferenced accessions and metadata standards.

Conclusions:

• TreeGenes provides a comprehensive platform for forest tree data management and analysis.
• The integrated approach facilitates comparative genomics and data visualization for researchers.
• The platform supports researchers in storing, submitting, and analyzing forest tree data effectively.