From Permits to Samples: Addressing Key Challenges for High‐Quality Reference Genome Generation in Europe
High-quality reference genome assemblies have become essential for deepening our understanding of biodiversity, yet obtaining them for many species remains surprisingly challenging. Drawing on experiences from the European Reference Genome Atlas (ERGA) community, we focus on permit and sample-handling procedures leading up to nucleic acid sequencing, covering tasks such as ensuring ethical and legal compliance, verifying accurate species identification, maintaining sample integrity during transport, and isolating high-quality DNA or nuclei. While many of the challenges and solutions we discuss are broadly relevant, our regulatory and logistical examples are primarily from Europe. By synthesising practical guidance, we highlight the crucial importance of taxonomic expertise, proper vouchering and biobanking, rigorous cold-chain management or alternative preservation methods, and emphasise adherence to packaging and shipping requirements for biological materials. We showcase examples spanning diverse regions, taxa and source materials, which underscore the importance of context-specific strategies and internationally harmonised protocols, particularly for metadata reporting. Our recommendations aim to support both small-scale projects and large initiatives, directing collective efforts to facilitate efficient sampling, vouchering and sample processing for future genomic studies.
Authors
- Claúdio Ciofi (ORCID: https://orcid.org/0000-0001-8537-8659)
- João Pimenta (ORCID: https://orcid.org/0000-0002-0989-8545)
- Rebekah A. Oomen (ORCID: https://orcid.org/0000-0002-2094-5592)
- Veronika N. Laine (ORCID: https://orcid.org/0000-0002-4516-7002)
- Michal Rindoš (ORCID: https://orcid.org/0000-0002-0836-5157)
- Jonas J. Astrin (ORCID: https://orcid.org/0000-0003-1961-1162)
- Elena Bužan (ORCID: https://orcid.org/0000-0003-0714-5301)
- Martina Pavlek (ORCID: https://orcid.org/0000-0001-6710-0581)
- Salvatore Tomasello (ORCID: https://orcid.org/0000-0001-5201-1156)
- Javier del Campo (ORCID: https://orcid.org/0000-0002-5292-1421)
- Robert Michael Waterhouse (ORCID: https://orcid.org/0000-0003-4199-9052)
- Ann McCartney (ORCID: https://orcid.org/0000-0001-5853-3772)
- Олександр Зіненко (ORCID: https://orcid.org/0000-0001-5228-9940)
- Camila J. Mazzoni (ORCID: https://orcid.org/0000-0001-6758-5427)
- Pradeep Kumar Divakar (ORCID: https://orcid.org/0000-0002-0300-0124)
- Leon Hilgers (ORCID: https://orcid.org/0000-0002-3539-2513)
- Katja Reichel (ORCID: https://orcid.org/0000-0001-9052-3179)
- Hampl
- Christian de Guttry (ORCID: https://orcid.org/0000-0002-4341-1200)
- Chiara Bortoluzzi
- Andrii Tarieiev
- Astrid Bohne
- Lada Lukić Bilela
- Jennifer Leonard
- Rita Monteiro
- Alexandra A.‐T. Weber
- Jaakko Pohjoismäki
- Ole Seehausen
- Camilla B. Di‐Nizo
- Jesus Lozano‐Fernandez
- José Melo‐Ferreira
- Olga Vinnere Pettersson
- Carola Greve
Institutions
- University of Sarajevo (BA)
- University of New Brunswick (CA)
- Goethe University Frankfurt (DE)
- University of Bern (CH)
- University of Primorska (SI)
- Universidad Complutense de Madrid (ES)
- Uppsala University (SE)
- SIB Swiss Institute of Bioinformatics (CH)
- Swedish Veterinary Agency (SE)
- University of Helsinki (FI)
- Universitat Pompeu Fabra (ES)
- University of Eastern Finland (FI)
- Universidade do Porto (PT)
- University of Oslo (NO)
- University of California, Santa Cruz (US)
- University of Agder (NO)
- Czech Academy of Sciences (CZ)
- Czech University of Life Sciences Prague (CZ)
- Charles University (CZ)
- Luther University (KR)
- Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE)
- Estación Biológica de Doñana (ES)
- Institute of Metrology of Bosnia and Herzegovina (BA)
- Zoological Research Museum Alexander Koenig (DE)
- Berlin Center for Genomics in Biodiversity Research (DE)
- College of Environmental Protection (SI)
- LOEWE Centre for Translational Biodiversity Genomics (DE)
- Institute of Entomology (CZ)
- Ruđer Bošković Institute (HR)
- Institut de Biologia Evolutiva (ES)
- Finnish Museum of Natural History (FI)
- Nordwestdeutsche Forstliche Versuchsanstalt (DE)
- Croatian Science Foundation (HR)
- Leibniz Institute for Zoo and Wildlife Research (DE)
- Czech Academy of Sciences, Biology Centre (CZ)
- Croatian Biospeleological Society
- University of Florence (IT)
- Swiss Federal Institute of Aquatic Science and Technology (CH)
- Martin Luther University Halle-Wittenberg (DE)
- Universitat de Barcelona (ES)
- University of Göttingen (DE)
- Freie Universität Berlin (DE)
- V. N. Karazin Kharkiv National University (UA)
- University of Gothenburg (SE)
Publication Details
- Journal
- Molecular Ecology Resources
- Published
- 2026-01-20
- DOI
- https://doi.org/10.1111/1755-0998.70100
- Primary Topic
- Environmental DNA in Biodiversity Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- UK Research and Innovation
- Ministerio de Ciencia, Innovación y Universidades
- New Brunswick Innovation Foundation
- European Commission
- Deutsche Forschungsgemeinschaft
- Vetenskapsrådet
- Freie Universität Berlin
- Science for Life Laboratory
- HORIZON EUROPE Framework Programme
- Natural Sciences and Engineering Research Council of Canada
- Fundação para a Ciência e a Tecnologia
- Staatssekretariat für Bildung, Forschung und Innovation
- European Regional Development Fund
- Agencia Estatal de Investigación
- Interreg