Evidence map›Paper›PMID 41560422›Full record

ReviewMolecular ecology resources2026

From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe.

Katja Reichel, Jaakko Pohjoismäki, Jonas J Astrin, Astrid Böhne, Chiara Bortoluzzi, Elena Bužan, Javier Del Campo, Claudio Ciofi, Camilla B Di-Nizo, Pradeep K Divakar and 23 more

Abstract readReview
In one paragraph

Review in Molecular ecology resources, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

33 authors.

Katja ReichelInstitute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany.ORCID https://orcid.org/0000-0001-9052-3179
Jaakko PohjoismäkiDepartment of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.ORCID https://orcid.org/0000-0002-1185-3610
Jonas J AstrinMuseum Koenig Bonn, LIB Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.ORCID https://orcid.org/0000-0003-1961-1162
Astrid BöhneMuseum Koenig Bonn, LIB Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.ORCID https://orcid.org/0000-0002-1284-3115
Chiara BortoluzziDepartment of Biology, University of Florence, Sesto Fiorentino (FI), Italy.ORCID https://orcid.org/0000-0001-6589-6635
Elena BužanFaculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia.ORCID https://orcid.org/0000-0003-0714-5301
Javier Del CampoInstitut de Biologia Evolutiva, Biodiversity Program, Universitat Pompeu Fabra, Barcelona, Spain.ORCID https://orcid.org/0000-0002-5292-1421
Claudio CiofiDepartment of Biology, University of Florence, Sesto Fiorentino (FI), Italy.ORCID https://orcid.org/0000-0001-8537-8659
Camilla B Di-NizoMuseum Koenig Bonn, LIB Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.ORCID https://orcid.org/0000-0002-6995-5994
Pradeep K DivakarFaculty of Pharmacy, Department of Pharmacology, Pharmacognosy and Botany, Complutense University of Madrid, Madrid, Spain.ORCID https://orcid.org/0000-0002-0300-0124
Carola GreveLOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.ORCID https://orcid.org/0000-0003-4993-1378
Vladimír HamplFaculty of Science, Department of Parasitology, BIOCEV, Charles University, Prague, Czech Republic.ORCID https://orcid.org/0000-0002-5430-7564
Leon HilgersLOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.ORCID https://orcid.org/0000-0002-3539-2513
Veronika N LaineFinnish Museum of Natural History, University of Helsinki, Helsinki, Finland.ORCID https://orcid.org/0000-0002-4516-7002
Jennifer A LeonardConservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain.ORCID https://orcid.org/0000-0003-0291-7819
Jesus Lozano-FernandezFacultat de Biologia, Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain.ORCID https://orcid.org/0000-0003-3597-1221
Lada Lukić BilelaFaculty of Science, Department of Biology, University of Sarajevo, Sarajevo, Bosnia and Herzegovina.ORCID https://orcid.org/0000-0001-7423-6284
Camila J MazzoniLeibniz Institut für Zoo- und Wildtierforschung, Berlin, Germany.ORCID https://orcid.org/0000-0001-6758-5427
Ann M McCartneyGenomics Institute, University of California, Santa Cruz, California, USA.ORCID https://orcid.org/0000-0003-3191-3200
José Melo-FerreiraDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.ORCID https://orcid.org/0000-0003-4473-1908
Rita MonteiroMuseum Koenig Bonn, LIB Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.ORCID https://orcid.org/0000-0003-1374-4474
Rebekah A OomenDepartment of Biological Sciences, University of New Brunswick, Saint John, New Brunswick, Canada.ORCID https://orcid.org/0000-0002-2094-5592
Martina PavlekRuder Boskovic Institute, Zagreb, Croatia.ORCID https://orcid.org/0000-0001-6710-0581
João PimentaCentro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.ORCID https://orcid.org/0000-0002-0989-8545
Michal RindosBiology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.ORCID https://orcid.org/0000-0002-0836-5157
Ole SeehausenDepartment of Fish Ecology & Evolution, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland.ORCID https://orcid.org/0000-0001-6598-1434
Andrii TarieievBüsgen-Institute, Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany.ORCID https://orcid.org/0000-0002-1123-7746
Salvatore TomaselloDepartment of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Göttingen, Göttingen, Germany.ORCID https://orcid.org/0000-0001-5201-1156
Olga Vinnere PetterssonUppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.ORCID https://orcid.org/0000-0002-5597-1870
Robert M WaterhouseEnvironmental Bioinformatics Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID https://orcid.org/0000-0003-4199-9052
Alexandra A-T WeberDepartment of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.ORCID https://orcid.org/0000-0002-7980-388X
Oleksandr ZinenkoV. N. Karazin Kharkiv National University, Kharkiv, Ukraine.ORCID https://orcid.org/0000-0001-5228-9940
Christian de GuttryEnvironmental Bioinformatics Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID https://orcid.org/0000-0002-4341-1200

Funding

Deutsche Forschungsgemeinschaft 530763738European Regional Development Fund Euro-MED0300730-C4NatureFundação para a Ciência e a TecnologiaHORIZON EUROPE Framework Programme 101059492Johanna Quandt Young AcademyMinisterio de Ciencia, Innovación y Universidades PID2023-147388NB-I00Ministerio de Ciencia, Innovación y Universidades PID2023-152577NB-I00Ministry of Education, Youth and Science 27-02-35-33087-6/24Natural Sciences and Engineering Research Council of Canada RGPIN-2024-06892New Brunswick Innovation Foundation TRF_2024_007Vetenskapsrådet 2021-05580
6 · The paper itself

Abstract

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.

Indexed as

GenomeGenomicsSpecimen HandlingEuropeSequence Analysis, DNADNA/RNA preservationeukaryotesEuropean Reference Genome Atlasgenome sequencinghigh molecular weight DNAsampling design

Identifiers

PMID41560422
PMCPMC12820446

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.