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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #402109

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Guidelines for standardizing gene model nomenclature and genome assembly quality metrics

Author
item CHOUGULE, KAPEEL - COLD SPRING HARBOR LABORATORY
item DYER, SARAH - EUROPEAN MOLECULAR BIOLOGY LABORATORY
item Cannon, Ethalinda

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: A reference genome typically starts from a single individual of a given species that is assembled from small sequencing reads. Subsequent increments that aim to improve genome quality and annotation (that is, where the genes are and what they encode) will incorporate more technologies and include more individuals, accessions/varieties/cultivars/breeds. How does one come up with a clear and unique identifier for each gene model from each genome assembly, and how best to assess the quality of assemblies and annotations? The AgBioData Genome and Gene Nomenclature Working Group is gathering input to understand community preferences regarding naming conventions and use of genome quality metrics, supporting the development of recommendations for agricultural genomics communities. We will present our findings to date.