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

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.

Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance

“…A permutation test ( n = 1000) was run for each model to determine a 5% significance level for LOD scores. Functional annotations for each gene associated with a significant SNP were obtained from the PILA.1_5.functionalannotations.tsv file at the TreeGenes database (treegenesdb.org) (Baker et al ., 2018; Falk et al ., 2018; Wegrzyn et al ., 2019). Annotations for SNPs represented by coding sequences were taken from the reference sugar pine genome V1.5, file CDS.FA from the TreeGenes database (Baker et al ., 2018; Falk et al ., 2018; Wegrzyn et al ., 2019).…”

A Reference Genome Sequence for Giant Sequoia

“…Translated UniGenes for all available gymnosperms were downloaded from the forest genomics database TreeGenes (https://treegenesdb.org/; Falk et al 2018;Wegrzyn et al 2019). The corresponding files from the Amborella trichopoda genome assembly were also included to provide an outgroup to the gymnosperm taxa.…”

Tripal MegaSearch: a tool for interactive and customizable query and download of big data

“…The Tripal MegaSearch module has been implemented in multiple databases including the Genome Database for Rosaceae ( www.rosaceae.org , 6 ), CottonGen ( www.cottongen.org , 7 ), the Citrus Genome Database ( www.citrusgenomedb.org ), Genome Database for Vaccinium ( www.vaccinium.org ), the Pulse Crop Database ( www.pulsedb.org ) and TreeGenes (treegene.org, 8 ). This MegaSearch Tripal extension module can be found along with the user documentation in the MainLab organization’s GitLab repository at https://gitlab.com/mainlabwsu and can also be accessed from https://tripal.readthedocs.io/en/latest/extensions/search.html#tripal-megasearch .…”