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Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
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2019 (English)In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, article id 813Article, review/survey (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019. Vol. 10, article id 813
Keywords [en]
database, content management system, forest tree, bioinformatics, web services
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-161586DOI: 10.3389/fpls.2019.00813ISI: 000473047200001OAI: oai:DiVA.org:umu-161586DiVA, id: diva2:1338360
Available from: 2019-07-22 Created: 2019-07-22 Last updated: 2019-07-22Bibliographically approved

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Mannapperuma, Chanaka
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Department of Plant PhysiologyUmeå Plant Science Centre (UPSC)
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