Scientists from 33 European countries join forces to generate reference genomes for the continent’s biological diversity

Establishing an inclusive, accessible, distributed and pan-European genomic infrastructure that could support the streamlined and scalable production of genomic resources for all European species. Credit: npj Biodiversity (2024). DOI: 10.1038/s44185-024-00054-6,

In a new publication, the European Reference Genome Atlas (ERGA) announces the success of its pilot project. This initiative assembled a large collaborative network of scientists and institutions across 33 countries to produce high-quality reference genomes of 98 European species—so far. The pilot project has provided valuable lessons and highlighted key challenges, positioning ERGA as a model for decentralized, inclusive and equitable biodiversity genomics initiatives around the world.

Among many of the project’s milestones are the first chromosome-level genome assemblies of species from Greece, one of Europe’s most biodiverse countries. Species such as the Cretan wall lizard (Podarcis cretensis) and Aristotle’s catfish (Silurus aristotelis) were sampled by local scientists in Greece to produce genomes that are now openly available for anyone across the world to access and study.

The findings are reported in an article published today in the journal npj Biodiversity.

These are but two examples of what can be achieved by uniting an international community of biodiversity scientists, fostering collaboration between and within countries. The ERGA pilot project emphasized equity and inclusion, with the goal that genomic research and resources are accessible to all, regardless of geographical origin. For many of the participating scientists and countries, the project offered the first opportunity to actively engage in the generation of state-of-the art reference genomic resources for their native biodiversity.

The ERGA pilot project was also successful in building momentum and bringing visibility to the growing importance of biodiversity genomics in Europe and beyond. Genomic data hold immense potential to inform conservation actions for endangered species and unlock discoveries in the fields of human health, bioeconomy, biosecurity and many other applications. For example, the greater argentine (Argentina silus) is among the species sequenced by the project—a commercially important fish species from the northern Atlantic.

This new reference genome will enable scientists to make more accurate assessments of the genetic status of the species’ populations, ultimately guiding management decisions to ensure that fishing practices are responsible and sustainable.

One of the species for which a high-quality reference genome is now also available for the first time is the white-tailed eagle (Haliaeetus albicilla). With this reference genome, it will be possible in future, for example, to investigate genetic disorders for which only the symptoms are currently known. This applies in particular to the so-called “pinching-off syndrome,” says bird of prey expert Dr. Oliver Krone from the Leibniz-IZW.

In this disease, the flight and control feathers of young white-tailed eagles are malformed and make flying impossible. The causes of this malformation of the feathers are genetic and are passed on recessively from both parent birds to the offspring. Furthermore, there are many possibilities to utilize the eagle genome for phylogenetic questions, Krone adds. For example, subpopulations could be differentiated from one another or isolated populations could be identified.

As the global scientific community strives to unlock the full potential of genomic data, the establishment of a Europe-wide collaborative network under the ERGA umbrella accelerates scientific progress and facilitates its translation into tangible benefits for biodiversity and society.

Additionally, the network helps scientists at all career stages to find and share opportunities for training, partnerships and funding. The ERGA pilot project was co-initiated in early 2021 by the then ERGA chair Dr. Camila Mazzoni from the Leibniz-IZW and the Berlin Center for Genomics in Biodiversity Research (BeGenDiv) who led calls with hundreds of genome scientists to set up and plan the collaborative project in an inclusive and decentralized way.

ERGA is the European node of the wider Earth BioGenome Project (EBP). In order to achieve its ambitious goal—to sequence all eukaryotic life on Earth—the EBP crucially needs worldwide participation and new, decentralized models of genome production.

The ERGA pilot project was able to show that a fully distributed, collaborative and coordinated genome production model is not only feasible but effective—even at a continental scale and without a central source of funding available. In fact, most of the project budget came from grassroots efforts by individual members and partnering institutions, with additional support from sequencing partners and commercial sequencing companies providing grants, discounts and in-kind contributions.

The ERGA pilot project helped to identify and address the many challenges of working at the international scale. These challenges include dealing with the legal and logistical hurdles of shipping biological samples across borders, resource disparities between countries and the search for balance between decentralization and the need for standardization to guarantee that only the highest possible reference genome assemblies which meet EBP metrics were produced by the project.

ERGA’s decentralized approach holds great promise for the future of biodiversity genomics. The pilot project’s success in building momentum and uniting researchers illustrates the power of this model.

By fostering international collaboration and focusing on inclusivity and equity, ERGA is setting new standards for biodiversity genomics. The lessons learned and the challenges identified and addressed in the pilot project will guide future efforts, promoting robust and standardized workflows and a comprehensive genomic database for species in Europe and beyond.

“The ERGA pilot demonstrated the importance of a well-connected scientific community that is willing to cooperate to achieve a major common goal. This success marks a significant milestone for ERGA, illustrating that such an initiative can be highly inclusive while still maintaining the high standards set by the Earth BioGenome Project (EBP) for reference genome production. This ERGA pilot project provides both an example and a roadmap for distributed efforts to build biogenomes across Europe and potentially beyond,” said Camila Mazzoni, former ERGA Chair and senior author of the article published—team leader “Evolutionary and conservation genomics” in the Leibniz-IZW Department of Evolutionary Genetics.

“The ERGA pilot project attempted to up-scale the generation of high-quality reference genomes across an entire continent. An endeavor of such magnitude was made possible only through its commitment to the principles of inclusion, equity and collaboration as well as the dedication of its diverse, transdisciplinary and cross-sectoral participants. I feel incredibly lucky to have worked alongside such an amazing group of colleagues to help kickstart the construction of a genomics encyclopedia of European species,” said Ann McCartney, Member of the ERGA Pilot Committee—Assistant Researcher at University of California Santa Cruz, and adjunct Assistant Professor at University College Dublin.

“When we took on the leadership of this project, we didn’t anticipate the extent of the work ahead. It was a challenging endeavor, but through perseverance and teamwork, we succeeded. We also had the invaluable support of sequencing centers, universities, and commercial companies who contributed to the ERGA pilot project, offering human resources for library creation, free sequencing and in-kind products. This experience was truly one of a kind,” said Alice Mouton, Member of the ERGA Pilot Committee—former FNRS postdoctoral researcher, and scientific collaborator at the University of Liège.

“ERGA was all a dream, until it wasn’t. Through this pilot project the prospect of uniting Europe under the flag of biodiversity genomics is now reality. We can be proud to have first established the process by which the genomes of many species will become available to the scientific community for conservation and beyond,” said Giulio Formenti, Member of the ERGA Pilot Committee—Research Assistant Professor at the Rockefeller University.

“The ERGA Pilot project is a significant milestone in the Earth BioGenome Project (EBP) and a major step forward for biodiversity genomics in Europe. As the first biodiversity genomics project coordinated at a continental scale, ERGA has demonstrated two fundamental principles on which the EBP was built—the first being that sequencing capacity will be geographically distributed, and the second being that any benefits derived from sequenced genomes would be shared equitably. ERGA is now poised to expand its goals to sequence thousands of genomes for conserving European biodiversity and the growth of a sustainable bioeconomy,” said Harris Lewin, Chair of the EBP Executive Council—Research Professor at ASU.

More information:
McCartney A. M. et al. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj Biodiversity (2024). DOI: 10.1038/s44185-024-00054-6, www.nature.com/articles/s44185-024-00054-6

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Leibniz Institute for Zoo and Wildlife Research

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Scientists from 33 European countries join forces to generate reference genomes for the continent’s biological diversity (2024, September 17)
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