Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection
The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA's pan-European network. To demonstrate the community's capability and capacity to realise ERGA's ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA's member base. SSP aims to aid participating researchers through (i) establishing standards for and collecting of sample/specimen metadata; (ii) prioritisation of species for genome sequencing; and (iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA's high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.
Authors
- José Melo‐Ferreira (ORCID: https://orcid.org/0000-0003-4473-1908)
- Ann M. Mc Cartney (ORCID: https://orcid.org/0000-0003-3191-3200)
- Astrid Böhne (ORCID: https://orcid.org/0000-0002-1284-3115)
- Rebekah A. Oomen (ORCID: https://orcid.org/0000-0002-2094-5592)
- Seanna McTaggart (ORCID: https://orcid.org/0000-0003-0977-4785)
- Rosa Fernández (ORCID: https://orcid.org/0000-0002-4719-6640)
- Olga Vinnere Pettersson (ORCID: https://orcid.org/0000-0002-5597-1870)
- Jennifer A. Leonard (ORCID: https://orcid.org/0000-0003-0291-7819)
- Torsten H. Struck (ORCID: https://orcid.org/0000-0003-3280-6239)
- Rita Monteiro (ORCID: https://orcid.org/0000-0003-1374-4474)
Institutions
- University of New Brunswick (CA)
- Universidade do Porto (PT)
- University of Oslo (NO)
- University of California, Santa Cruz (US)
- University of Agder (NO)
- Norwich Research Park (GB)
- Science for Life Laboratory (SE)
- Leibniz Association (DE)
- Estación Biológica de Doñana (ES)
- Zoological Research Museum Alexander Koenig (DE)
- Earlham Institute (GB)
- Institut de Biologia Evolutiva (ES)
- University of Gothenburg (SE)
Publication Details
- Journal
- npj Biodiversity
- Published
- 2024-09-17
- DOI
- https://doi.org/10.1038/s44185-024-00053-7
- Citations
- 9
- Primary Topic
- Environmental DNA in Biodiversity Studies
- Type
- article
- Field-Weighted Citation Impact
- 4.13
Funders
- James S. McDonnell Foundation
- UK Research and Innovation
- Deutsche Forschungsgemeinschaft
- Rural Development Administration
- Ministerio de Ciencia e Innovación
- Norges Forskningsråd
- Science for Life Laboratory
- Leibniz-Institut für Zoo- und Wildtierforschung
- Directorate for Biological Sciences
- HORIZON EUROPE Framework Programme
- Natural Sciences and Engineering Research Council of Canada
- Biotechnology and Biological Sciences Research Council
- Leibniz-Gemeinschaft
- Fundação para a Ciência e a Tecnologia
- Staatssekretariat für Bildung, Forschung und Innovation
- Agencia Estatal de Investigación
- European Social Fund
- HORIZON EUROPE European Research Council