A Novel Tripal Database Module and Workflow to Facilitate Variant Mapping and Detection in Non-Model Plant Species

Single nucleotide polymorphisms (SNPs) are detected in a variety of plant genomic and transcriptomic datasets to enable landscape genomes, ecological genomics, and association mapping to phenotypes of interest. These sources of variation are critical to address questions related to breeding and adaptation. The TreeGenes database and Hardwood Genomics Web represent web-based genomic repositories for forest trees. Together, they represent over two thousand species, of which the vast majority do not have a reference genome. SNP detection in these species often originates in transcriptomes, exome capture, GBS fragments, or similar RAD-Seq assemblies. The target objects are poorly referenced and the conversion of variants from one resource to another quickly becomes prohibitive. To facilitate the alignment of existing calls onto new genomic or transcriptomic assemblies, we are developing a web-based workflow. Implementation of this workflow is enabled through the Tripal Gateway which integrates the Galaxy API with efficient data transfer to enable analysis on high performance computing resources. The workflow is designed to take VCF formatted variant calls with the original reference genomic or transcriptomic resource from the user. The user has the option to select an existing transcriptome or genome, or provide a new target object. Existing variants can be re-mapped and/or new variation detected if the SRA (raw read) accessions are also provided. This comprehensive pipeline allows the user to customize mapping and variant call parameters as well as connect the new variant calls with individual tree accessions that are associated with phenotypic and/or environmental data.