Functional Annotation at Scale: Pipelined Analysis of Phytozome Data and Results from Large Inter-Species Comparisons.

Phytozome, the Joint Genome Institute’s portal for Comparative Plant Genomics, hosts ~60 assembled and annotated plant genomes, drawn from a broad range of Viridiplantae species with relevance to biofuels, climate change adaptation, and plant evolution. Approximately two-thirds of these genomes were assembled and/or annotated at the JGI, with the remainder acquired from external sources.

As a centralized integrated database, Phytozome enables large scale classification and analysis of plant genomic data using consistent, versioned and well-defined protocols. We have recently incorporated InterProScan v5 and the PlantCyc system into our automated functional analysis workflows, using the Nextflow system to handle pipelining and parallelization tasks. Nextflow allows us to bypass certain issues with deploying InterProScan on SGE-based compute clusters, and provides a uniform workflow platform for most of our computational pipelines.

Together with our systematic computation of gene orthologs between organism pairs and our RNA-seq based expression pipelines, we provide a rich set of comparative tools and data for the functional annotation of all Phytozome proteins. We illustrate the utility of the database for functional annotation through the use of gene expression, orthology, and pathway mapping to compare imputed function in both model and non-model plant systems.