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Wegrzyn JL, Staton MA, Street NR, Main D, Grau E, Herndon N, Buehler S, Falk T, Zaman S, Ramnath R, Richter P, Sun L, Condon B, Almsaeed A, Chen M, Mannapperuma C, Jung S, Ficklin S. Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. FRONTIERS IN PLANT SCIENCE 2019; 10:813. [PMID: 31293610 PMCID: PMC6603172 DOI: 10.3389/fpls.2019.00813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 06/05/2019] [Indexed: 05/11/2023]
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.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Margaret A. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Emily Grau
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Nic Herndon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Sean Buehler
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Risharde Ramnath
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Peter Richter
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Lang Sun
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, United States
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