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Research Project: Mitigating Disease and Stress in Honey Bee Colonies

Location: Bee Research Laboratory

Title: Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation

Author
item LAWNICZAK, MARA K. N. - Wellcome Trust Sanger Institute
item KOCOT, KEVIN M. - University Of Alabama
item ASTRIN, JONAS J. - Leibniz Institute
item BLAXTER, MARK - Wellcome Trust Sanger Institute
item SOTERO-CAIO, CIBELE G. - Wellcome Trust Sanger Institute
item BARKER, KATHARINE B. - Smithsonian Institute
item Childers, Anna
item CODDINGTON, JONATHAN - Smithsonian Institute
item DAVIS, PAUL - Wellcome Trust Sanger Institute
item HOWE, KERSTIN - Wellcome Trust Sanger Institute
item JOHNSON, WARREN E. - Smithsonian Institute
item MCKENNA, DUANE D. - University Of Memphis
item WIDEMAN, JEREMY G. - Arizona State University
item PETTERSSON, VINNERE - Uppsala University
item RAS, VERENA - University Of The Western Cape
item SANTOS, BERNARDO F. - Leibniz Institute

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/13/2025
Publication Date: 5/29/2025
Citation: Lawniczak, M., Kocot, K., Astrin, J., Blaxter, M., Sotero-Caio, C., Barker, K., Childers, A.K., Coddington, J., Davis, P., Howe, K., Johnson, W., Mckenna, D., Wideman, J., Pettersson, V., Ras, V., Santos, B. 2025. Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation. Gigascience. 14. Article egiaf041. https://doi.org/10.1093/gigascience/giaf041.
DOI: https://doi.org/10.1093/gigascience/giaf041

Interpretive Summary: The Earth BioGenome Project is an international network of genome sequencing projects that collectively aim to sequence all species across the Tree of Life. Genome assemblies of the highest quality that are accompanied by robust data about the specimen and methodology will be the most useful as enduring resources for future research. To produce a reference-level genome assembly, many factors should be considered prior to collecting samples. This article serves as a guide to researchers interested in sequencing genomes that meet the high standards of the Earth BioGenome Project. It contains updated recommended standards and considerations for sample collection and processing as well as known challenges that will need to be addressed. By following up-to-date best practices researchers will be more successful in generating the best genome assembly possible.

Technical Abstract: The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Life. Currently in its first phase, the project is targeting family-level representatives and is progressing rapidly. Here we outline recommended standards and considerations in sample acquisition and processing for those involved in biodiverse reference genome creation. These standards and recommendations will evolve with advances in related processes. Additionally, we discuss the challenges raised by the ambitions for later phases of the project, highlighting topics related to sample collection and processing that require further development.