Gene nomenclature by default, or BLASTing to Babel

Area of Science:

• Genomics
• Bioinformatics
• Comparative Genomics

Background:

• Mammalian genome sequencing projects are rapidly expanding.
• Gene nomenclature often relies on homology searches like BLAST against annotated genomes.
• This practice can lead to naming inconsistencies, especially when direct orthologs are absent.

Purpose of the Study:

• To highlight a critical issue in mammalian gene nomenclature.
• To address the problem of inaccurate gene naming due to reliance on BLAST homology.
• To examine the consequences of using BLAST best hits for naming genes across species.

Main Methods:

• Analysis of gene naming conventions in mammalian genomes.
• Comparative genomics approach focusing on rat and mouse genomes.
• Case study using rat cytochrome P450 (Cyp) gene family.

Main Results:

• Reliance on BLAST best hits for gene naming causes significant nomenclature issues.
• Rat gene nomenclature frequently misidentifies paralogs as orthologs due to mouse genome reliance.
• Inaccurate gene names, including for rat Cyp genes, are appearing in public genome browsers.

Conclusions:

• Current gene naming practices based on BLAST homology are flawed and lead to widespread inaccuracies.
• The reliance on cross-species gene name sharing creates a false sense of orthology.
• Urgent revision of mammalian gene nomenclature strategies is needed to ensure accuracy and prevent duplicate naming.