Integrating the biodiversity genomics continuum: harmonising data from barcodes to reference genomes

Research Ideas and Outcomes, vol. 12

Abstract

Biodiversity genomics is converging from historically separate approaches — DNA barcoding and reference genome sequencing — into an integrated digital ecosystem driven by shared data stewardship principles: transparent provenance, persistent identifiers and interoperable repositories. We demonstrate how these workflows can operate within a unified informatics architecture spanning data generation, validation, publication and reuse. We describe coordinated infrastructure, including the European BOLD mirror, ERGA Genome Tracking Console and metadata platforms COPO and PlutoF. These systems employ harmonised validation pipelines, shared metadata standards that bridge the Darwin Core and Genomic Standards Consortium vocabularies and automated data exchange amongst ENA, UNITE and GBIF. Workflows in Galaxy, Nextflow and Snakemake are registered in WorkflowHub as Research Object Crates (RO-Crates), ensuring reproducibility and complete provenance. Key outcomes include comprehensive data flow documentation, automated quality control using BUSCO and ERGA Assembly Reports and robust specimen-to-data linkage. We identify challenges in metadata harmonisation, distributed tracking, collaborative attribution and infrastructure sustainability and provide recommendations for addressing them through existing platforms and emerging RO-Crate standards. This work establishes practical foundations for treating biodiversity molecular data as a continuum, demonstrating how FAIR principles can scale to continental initiatives.

Authors 20

1. Katharina F. Heil

   ELIXIR

   Affiliation as printed

   ELIXIR Europe, Hinxton, Cambridge, United Kingdom

2. Tyler Alioto

   Centro Nacional de Análisis Genómico

   Affiliation as printed

   Centro Nacional de Análisis Genómico, Barcelona, Spain

3. Astrid Böhne

   Leibniz Institute for the Analysis of Biodiversity Change

   Affiliation as printed

   Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Bonn, Germany

4. Tom Brown

   Berlin Center for Genomics in Biodiversity Research · Leibniz Institute for Zoo and Wildlife Research

   Affiliation as printed

   Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany, Berlin, Germany

   Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany, Berlin, Germany

5. Physilia Chua

   ELIXIR

   Affiliation as printed

   ELIXIR Europe, Hinxton, Cambridge, United Kingdom

6. Christian de Guttry

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland

7. Diego N. De Panis

   Berlin Center for Genomics in Biodiversity Research · Leibniz Institute for Zoo and Wildlife Research

   Affiliation as printed

   Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Str 6-8, 14195, Berlin, Germany

   Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str 17, 10315, Berlin, Germany

8. C Raymond Goble

   University of Manchester

   Affiliation as printed

   School of Computer Science, University of Manchester, Manchester, United Kingdom

9. Ivo Gut

   Centro Nacional de Análisis Genómico

   Affiliation as printed

   Centro Nacional de Análisis Genómico, Barcelona, Spain

10. Marta Ortova Gut

    Centro Nacional de Análisis Genómico

    Affiliation as printed

    Centro Nacional de Análisis Genómico, Barcelona, Spain

11. Nick Juty

    University of Manchester

    Affiliation as printed

    University of Manchester, Manchester, United Kingdom

12. Seanna J. McTaggart

    Earlham Institute

    Affiliation as printed

    Earlham Institute, Norwich, United Kingdom

13. Laura Alejandra Nájera-cortazar
    Affiliation as printed

    BIOPOLIS Association CIBIO, Vairão, Portugal

14. Joana Paupério

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom

15. Tomasz Rewicz

    University of Łódź

    Affiliation as printed

    University of Lodz, Lodz, Poland

16. Felix Shaw

    Earlham Institute

    Affiliation as printed

    Earlham Institute, Norwich, United Kingdom

17. Stian Soiland-Reyes

    University of Manchester

    Affiliation as printed

    The University of Manchester, Manchester, United Kingdom

18. Robert Michael Waterhouse

    SIB Swiss Institute of Bioinformatics

    Affiliation as printed

    SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland

19. Peter M. Woollard
    Affiliation as printed

    European Molecular Biology Laboratory, Cambridge, United Kingdom

20. Rutger Vos Aachen Naturalis Biodiversity Center

    Naturalis Biodiversity Center

    Affiliation as printed

    Naturalis Biodiversity Center, Leiden, Netherlands