Growing and cultivating the forest genomics database, TreeGenes.

Taylor Falk,Doreen Main,Sumaira Zaman,Margaret Staton,Stephen Ficklin,Sook Jung,Frank A Feltus,Risharde Ramnath,Peter Richter,Emily Grau,Nic Herndon,Eliza M Baker,Jill L Wegrzyn,Sean Buehler

doi:10.1093/database/bay084

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.

Highlights

The availability of high-throughput sequencing has enabled the assembly of over 4500 eukaryote genomes in the past 10 years [8]
TreeGenes has become a part of the federation of Tripal databases and has developed modules focused on cross-site querying, data transfer and direct access to analytical tools that serve the unique forest tree community
The TreeGenes database has served the forest genetics community since the early 1990s. It was implemented first as Dendrome, a repository to hold information related to genetic linkage maps and the researchers who generated them

Summary

Introduction

The availability of high-throughput sequencing has enabled the assembly of over 4500 eukaryote genomes in the past 10 years [8]. Vol 2018, Article ID bay084 relevant metadata standards and integrated analytical frameworks, TreeGenes provides a platform for researchers to store, submit and analyze forest tree data. TreeGenes has become a part of the federation of Tripal databases and has developed modules focused on cross-site querying, data transfer and direct access to analytical tools that serve the unique forest tree community.

Results

Conclusion