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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #415243

Research Project: MaizeGDB - Database and Computational Resources for Maize Genetics, Genomics, and Breeding Research

Location: Corn Insects and Crop Genetics Research

Title: Guidelines for gene and genome assembly nomenclature

Author
item Cannon, Ethalinda
item Molik, David
item WRIGHT, ADAM - Ontario Cancer Institute
item ZHANG, HUITING - Washington Tree Fruit Research Commission
item Honaas, Loren
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item DYER, SARAH - Embl-Ebi

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2024
Publication Date: 1/15/2025
Citation: Cannon, E.K., Molik, D.C., Wright, A., Zhang, H., Honaas, L.A., Chougule, K., Dyer, S. 2025. Guidelines for gene and genome assembly nomenclature. Genetics. https://doi.org/10.1093/genetics/iyaf006.
DOI: https://doi.org/10.1093/genetics/iyaf006

Interpretive Summary: Two individuals within a species have unique genetics. To study all genetic differences within a species, it is important to have the genome sequences and predicted genes ("gene models") for several different individuals. Conducting research with the resulting data is challenging if the names of the genome sequences and gene models don't follow consistent naming patterns. This paper explores the problems of inconsistent naming and presents a recommendation for clearly naming genome sequences and gene models.

Technical Abstract: The rapid increase in reference-quality genome assemblies and gene model annotations presents powerful new opportunities for research. However, inconsistencies in naming conventions can create difficulties in identifying appropriate assemblies and their versions, in linking gene models to annotation analyses and assemblies, and in developing and running analysis pipelines that can correctly interpret multiple nomenclature rules. Here we explore the challenges of genomic nomenclature and give a recommendation for consistent nomenclature that is broadly applicable for all species.