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

In a new publication, the European Reference Genome Atlas (ERGA) announces the success of its pilot project. This initiative brought together a large collaborative network of scientists and institutions from 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 worldwide.

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

The results are reported in a paper published today in the journal Biodiversity npj.

These are just 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 focused on equity and inclusion, with the goal of making genomic research and resources accessible to all, regardless of geographic origin. For many participating scientists and countries, the project provided the first opportunity to actively engage in the production of cutting-edge reference genomic resources for their native biodiversity.

The ERGA pilot project has also succeeded in building momentum and highlighting the growing importance of biodiversity genomics in Europe and beyond. Genomic data hold immense potential to inform conservation actions for threatened species and open the door to discoveries in human health, bioeconomy, biosecurity and many other applications. For example, the Argentinian silus (Argentina silus) is among the species sequenced by the project, a commercially important fish species from the North Atlantic.

This new reference genome will allow scientists to more accurately assess the genetic status of the species' populations, thereby guiding management decisions to ensure that fishing practices are responsible and sustainable.

The white-tailed eagle (Haliaeetus albicilla) is one of the species for which a high-quality reference genome is now available for the first time. Thanks to this reference genome, it will now be possible to study, for example, genetic diseases for which only the symptoms are currently known. This applies in particular to the so-called “pinching syndrome”, explains Dr. Oliver Krone, a bird of prey specialist at the Leibniz-IZW.

In this disease, the flight and control feathers of young white-tailed eagles are malformed and prevent them from flying. The causes of this feather malformation are genetic and are transmitted recessively from both parents to the offspring. In addition, there are many possibilities to use the eagle genome for phylogenetic questions, adds Krone. For example, subpopulations could be differentiated from each other or isolated populations could be identified.

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

In addition, the network helps scientists at all stages of their careers find and share training, partnership and funding opportunities. The ERGA pilot project was launched in early 2021 by ERGA Chair Dr. Camila Mazzoni of 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 Earth BioGenome Project (EBP). To achieve its ambitious goal – to sequence all eukaryotic life on Earth – the EBP absolutely needs global participation and new decentralized models of genome production.

The ERGA pilot project was able to demonstrate that a fully distributed, collaborative and coordinated genome production model is not only feasible but also effective, even on a continental scale and without a central source of funding. In fact, the majority of the project budget came from the core efforts of individual members and partner institutions, with additional support from sequencing partners and commercial sequencing companies providing grants, rebates and in-kind contributions.

The ERGA pilot project identified and addressed the many challenges of working internationally. These challenges include managing the legal and logistical hurdles of shipping biological samples across borders, resource disparities between countries, and balancing decentralization with the need for standardization to ensure that only the highest possible reference genome assemblies, consistent with EBP parameters, are produced by the project.

ERGA's decentralized approach holds great promise for the future of biodiversity genomics. The success of the pilot project, which helped build momentum and unite researchers, illustrates the power of this model.

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

“The ERGA pilot project has demonstrated the importance of a well-connected scientific community willing to cooperate to achieve a major common goal. This success marks an important milestone for ERGA, illustrating that such an initiative can be highly inclusive while maintaining the high standards set by the Earth BioGenome Project (EBP) for the production of reference genomes. 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 President and lead author of the published paper, Team Leader “Evolutionary and Conservation Genomics” at the Department of Evolutionary Genetics Leibniz-IZW.

“The ERGA Pilot Project sought to scale up the production of high-quality reference genomes across an entire continent. An undertaking of this magnitude was only possible because of its commitment to the principles of inclusion, equity, and collaboration, and the dedication of its diverse, transdisciplinary, and cross-sectoral participants. I feel incredibly fortunate to have worked alongside such a formidable group of colleagues to help pioneer the construction of a genomic encyclopedia of European species,” said ERGA Pilot Committee member Ann McCartney, Adjunct Research Scientist at the University of California, Santa Cruz, and Adjunct Assistant Professor at University College Dublin.

“When we took over the leadership of this project, we did not anticipate the scale of the work that lay ahead. It was a huge challenge, but through perseverance and teamwork, we succeeded. We also benefited from the invaluable support of the sequencing centres, universities and commercial companies that contributed to the ERGA pilot project, offering human resources for library creation, free sequencing and in-kind products. This experience was truly unique,” ​​said Alice Mouton, member of the ERGA steering committee, former FNRS postdoctoral researcher and scientific collaborator at the University of Liège.

“ERGA was a dream, until it wasn’t. With this pilot project, the prospect of uniting Europe under the banner of biodiversity genomics is now a reality. We can be proud to have pioneered the process by which the genomes of many species will be made available to the scientific community for conservation and beyond,” said Giulio Formenti, ERGA Steering Committee member and Assistant Research Professor at The Rockefeller University.

“The ERGA pilot project is a milestone in the Earth BioGenome Project (EBP) and a major step forward for biodiversity genomics in Europe. As the first coordinated biodiversity genomics project on a continental scale, ERGA has demonstrated two core principles on which EBP was built: the first being that sequencing capacity will be geographically distributed, and the second being that any benefits derived from sequenced genomes will be shared equitably. ERGA is now poised to expand its goals to sequencing thousands of genomes for the conservation of European biodiversity and the growth of a sustainable bioeconomy,” said Harris Lewin, chair of the EBP Executive Board and a research professor at ASU.