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Gene Ontology Meta Annotator for Plants (GOMAP).

Kokulapalan Wimalanathan1,2,3, Carolyn J Lawrence-Dill4,5,6

  • 1Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50010, USA. kokul@bioinformapping.com.

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Summary

The Gene Ontology Meta Annotator for Plants (GOMAP) pipeline enhances plant genome annotation efficiency and accuracy. This tool improves gene function predictions for large, complex plant genomes, aiding biological research.

Keywords:
CAFAFunctional annotationGene ontologyPlant genomes

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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.