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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens.

Helder Pedro¹, Andrew D Yates¹, Paul J Kersey¹

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.

Frontiers in Microbiology

|December 3, 2019

Summary

Community-driven genomic annotation efforts, like those for Botrytis cinerea and Blumeria graminis, create accurate gene sets. This collaborative approach accelerates plant disease research by unifying data and expertise.

Keywords:

Ensembl genomes apollo community gene annotation fungi plant pathogens

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Area of Science:

Genomics and Bioinformatics
Plant Pathology
Computational Biology

Background:

Accurate genomic annotation is crucial for managing plant diseases.
Key plant pathogens often have incomplete or inconsistent gene sets, hindering research.
Lack of dedicated funding and teams exacerbates annotation issues.

Purpose of the Study:

To describe a collaborative, community-driven approach to improve genomic annotation for plant pathogens.
To address the shortcomings of incomplete and inconsistent gene sets in important plant pathogens.
To foster collaboration and accelerate research through unified, well-annotated genomic data.

Main Methods:

Engaged over 40 members of the Botrytis cinerea research community from eight countries.
Utilized the Apollo gene editing tool for systematic review of the entire gene set (11,707 protein-coding genes).
Applied a similar community-driven curation process to Blumeria graminis f. sp. hordei and are initiating it for Zymoseptoria tritici.

Main Results:

Successfully generated a systematically reviewed and disseminated gene set for Botrytis cinerea within 6-7 months.
Achieved a completely redefined gene set for Blumeria graminis f. sp. hordei.
Demonstrated the value of community agreement and ownership in accelerating research.

Conclusions:

Community-driven annotation efforts yield improved and accurate gene sets for plant pathogens.
Collaborative curation fosters ownership and accelerates research progress in the field.
Unifying divergent datasets and research teams through community efforts enhances data quality and benefits related species and automated prediction tools.