Gene Ontology Meta Annotator for Plants (GOMAP).

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Accurate gene annotation is crucial for understanding genome function and enabling biological inference.
• Gene Ontology (GO) term assignment is a standard for functional annotation, with ongoing improvements in prediction methods.

Purpose of the Study:

• To present the Gene Ontology Meta Annotator for Plants (GOMAP) pipeline for high-throughput, reproducible, genome-scale GO annotation in plants.
• To optimize GOMAP for performance in High-Performance Computing (HPC) environments and ensure portability via containerization.

Main Methods:

• Containerization of the GOMAP pipeline using Singularity for enhanced portability and reproducibility.
• Optimization of GOMAP for High-Performance Computing (HPC) environments to handle large plant genomes.
• Application of GOMAP to annotate multiple maize genomes as a case study.

Main Results:

• GOMAP successfully annotated large, repetitive plant genomes, including multiple maize accessions.
• The pipeline demonstrated improvements in the number of annotated genes and the quality of GO assignments per gene.
• GOMAP has been successfully deployed for annotating other plant species like wheat, rice, barley, cotton, and soy.

Conclusions:

• GOMAP provides an optimized, high-throughput, and reproducible solution for plant genome-scale functional annotation.
• The containerized pipeline enhances accessibility and performance, particularly for large and complex plant genomes.
• GOMAP significantly expands and improves the quality of GO annotations, supporting plant biology research.