Gene Ontology Meta Annotator for Plants

Annotating gene structures and functions to genome assemblies is a must to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most pervasively used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions.

GOMAP, the Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation for plant genomes. GOMAP’s methods have been shown to expand and improve the number of genes annotated and annotations assigned per gene as well as the quality (based on F-score) of GO assignments in maize.

Here we report on the pipeline’s availability and performance for annotating large, repetitive plant genomes and describe how to deploy GOMAP to annotate additional plant genomes. We containerized GOMAP to increase portability and reproducibility, and optimized its performance for HPC environments. GOMAP has been used to annotate multiple maize lines, and is currently being deployed to annotate other species including wheat, rice, barley, cotton, soy, and others.

Instructions along with access to the GOMAP Singularity container are freely available online at https://gomap-singularity.readthedocs.io/en/latest/.

A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/gomap-datasets/.