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. 2019 Jun 25;10:813.
doi: 10.3389/fpls.2019.00813. eCollection 2019.

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

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Free PMC article

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

Jill L Wegrzyn et al. Front Plant Sci. .
Free PMC article

Abstract

Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.

Keywords: bioinformatics; content management system; database; forest tree; web services.

Figures

FIGURE 1
FIGURE 1
PlantGenIE, TreeGenes, and Hardwood Genomics Project represent integrated web-based frameworks that rely on a combination of primary repositories, secondary plant comparative databases, and user submissions to provide further value through data curation, integration, and analytics.

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