Community standards for genomic resources, genetic conservation, and data integration

Abstract

Genetics and genomics are increasingly important in forestry management and conservation. Next generation sequencing can increase analytical power, but still relies on building on the structure of previously acquired data. Data standards and data sharing allow the community to maximize the analytical power of high throughput genomics data. The landscape of incomplete submissions, minimal metadata, and distributed raw data inhibits aspects of data re-use, validation, and discovery. Community databases can address these challenges for their research communities by collecting and integrating data, as well as providing analytical tools. The Hardwood Genomics Web (HWG, http://www.hardwoodgenomics.org) and TreeGenes Database (http://treegenesdb.org) are community resources for forest tree genetics research. These web-based repositories host a variety of data types, including genome sequences, transcriptomes, genetic maps, and supporting marker information for 23 tree species in HWG and another 1780 species in TreeGenes. TreeGenes and the HWG host data visualization and analytical tools to further integrate and interrogate these datasets. Specific analytical functions include gene expression, functional annotation, and association genetics.

Parent Publication

• Gene conservation of tree species—banking on the future. Proceedings of a workshop.

Citation

Wegrzyn, Jill; Staton, Meg; Grau, Emily; Cronn, Richard; Nelson, C. Dana. 2017. Community standards for genomic resources, genetic conservation, and data integration. In: Sniezko, Richard A.; Man, Gary; Hipkins, Valerie; Woeste, Keith; Gwaze, David; Kliejunas, John T.; McTeague, Brianna A., tech. cords. 2017. Gene conservation of tree species—banking on the future. Proceedings of a workshop. Gen. Tech. Rep. PNW-GTR-963. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station: 28-29.