Protocol for creating a gene dictionary for organelle genomes using the Gene Dictionary Tool

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Fungal mitochondrial genomes require accurate gene annotation for comprehensive analysis.
• Existing methods for gene dictionary creation can be cumbersome and lack standardization.

Purpose of the Study:

• To present a standardized protocol for generating gene dictionaries for fungal mitochondrial genomes.
• To develop a user-friendly tool that facilitates the annotation of missing genes.

Main Methods:

• Utilizing a Python Command Line Interface (CLI) to identify annotation gaps.
• Employing two Jupyter Notebooks to construct the gene dictionary from GFF3 files.
• The Gene Dictionary Tool is central to the protocol.

Main Results:

• A .gdict file is generated as the final output, adhering to FAIR data principles.
• The protocol successfully creates a comprehensive gene dictionary for fungal mitochondrial genomes.
• The process is streamlined through automated identification of annotation needs.

Conclusions:

• The presented protocol offers an efficient and reproducible method for fungal mitochondrial genome annotation.
• The generated gene dictionaries are FAIR-compliant, promoting data sharing and reuse.
• This adaptable protocol can be applied to other genomic datasets beyond fungi.