Location: Corn Insects and Crop Genetics Research
Title: Guidelines for gene and genome assembly nomenclatureAuthor
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Cannon, Ethalinda |
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Molik, David |
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WRIGHT, ADAM - Ontario Cancer Institute |
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ZHANG, HUITING - Washington Tree Fruit Research Commission |
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Honaas, Loren |
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CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory |
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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. |