A new study led by the European Reference Genome Atlas (ERGA) consortium brings together in its pilot project a large collaborative network of researchers and institutions in 33 countries to produce high-quality reference genomes of 98 European species. The Institute of Evolutionary Biology (IBE), a joint centre of the Spanish National Research Council (CSIC) and the Pompeu Fabra University (UPF), has played a fundamental role as the genomic node of the pilot, participating in the establishment of the highest standard for the sequencing of the species studied, both vertebrates and invertebrates. The cutting-edge genomics work developed, which has been led by IBE researcher Rosa Fernández, has allowed genomes to be sequenced with unprecedented precision for key species of European biodiversity and can be applied to many more in the future within the consortium, ERGA.

The pioneering initiative, which has proven to be a success, marks a significant milestone in creating a database of reference genomes of the highest quality for all European animals, plants, and fungi. 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, as reported in a new collection of research papers published today in npj Biodiversity.

The IBE: key ERGA node for the next-generation genomics of the pilot project

One of the biggest challenges facing the consortium was to establish a quality standard in the extraction and processing of DNA (nucleic acids) for all the species in the project, which would allow for maximum quality sequencing and data analysis and could be shared within the scientific community. Rosa Fernández, IBE principal investigator in the Metazoa Phylogenomics laboratory, participated in the establishment of this standard, raising the quality of genomes to chromosomal-level precision.

Until now, many of the genomic efforts have used techniques such as Illumina, PacBio, or Nanopore, capable of analyzing short or long DNA sequences that must subsequently be assembled to reconstruct the genome of the species studied. But this is not enough to have a genome of the highest quality. The IBE team has taken a step forward by using the novel Hi-C technique, which allows the sequencing of complete chromosomes and reconstructing the three-dimensional structure of the genome, optimizing protocols for non-model species that are complicated to process in the laboratory.

“The genome is packaged like a ball inside the cell nucleus. With this new technique, we are able to “undo” and “read” the tangle, chromosome by chromosome. In addition, we preserve the folding’s information, which is key to deciphering how the genome is assembled and above all to being able to reconstruct its three-dimensional structure,” explains Fernández.

Fernández's team at the IBE, led by Judit Salces-Ortiz and Nuria Escudero as key players in the optimization of the protocols, participated in the sequencing of more than 14 genomes of the pilot project, accompanying various European groups in the development of the technique, both in vertebrate and invertebrate species.

An example of teamwork for biodiversity genomics

Among the many milestones of the project are the first genomic assemblies at the chromosome level of species from Greece, one of the most biodiverse countries in Europe. Species such as the Cretan lizard and Aristotle's catfish were sampled by local researchers in Greece to produce genomes that are now available for anyone around the world to access and study. “This is a great example of what can be achieved by uniting an international community of biodiversity researchers, fostering collaboration between and within countries,” adds Rosa Fernández, currently a member of the ERGA executive committee.

Other IBE researchers, such as Javier del Campo, have also participated in the pilot. Other CSIC centers have also participated, such as the National Museum of Natural Sciences (MNCN-CSIC), the Doñana Biological Station (EBD-CSIC) or the Botanical Institute of Barcelona (IBB-CSIC), as well as the National Analysis Center Genomics (CNAG) and the Barcelona Supercomputing Center (BSC), among others.

The ERGA pilot project focuses on equity and inclusion, with the goal of making genomic research and resources accessible to all, regardless of geographic borders. For many of the participating countries and researchers, the project offered the first opportunity to actively participate in the generation of next-generation reference genomic resources for their local native biodiversity.

European effort with global impact on planetary well-being

The ERGA pilot project also managed to generate momentum and give visibility to the growing importance of biodiversity genomics in Europe and other continents. Genomic data has immense potential to inform conservation actions for endangered species and generate discoveries in the fields of evolution, human health, bioeconomics, biosecurity, and many other applications. Among the species sequenced by the project is, for example, the Argentine grouper, a commercially important fish species from the North Atlantic. This new reference genome will allow scientists to make more accurate assessments of the genetic status of the species populations, ultimately guiding management decisions to ensure that fishing practices are sustainable and responsible.

As the global scientific community strives to harness the full potential of genomic data, the creation of a European-wide collaborative network under the ERGA umbrella accelerates scientific progress and facilitates its translation into tangible benefits for biodiversity. Additionally, the network helps researchers at all stages of their careers find and share training, collaboration, and funding opportunities.

ERGA, part of the Earth BioGenoma project (EBP)

ERGA is the European node of the Earth BioGenoma Project (EBP). To achieve its ambitious goal (sequencing all eukaryotic life on Earth), the EBP crucially needs global participation in our decentralized genome production models. The ERGA pilot project has demonstrated that a fully distributed, collaborative, and coordinated genome production model is not only feasible but also effective, finally on a continental scale and without a central source of financing available. In fact, the majority of the project's budget will come from the efforts of individual members and partner institutions, with additional support from sequencing partners and commercial sequencing companies that will provide various contributions.

The ERGA pilot project will help identify and address the many challenges involved in working on an international scale. These challenges include the legal and logistical obstacles involved in sending biological samples across borders, resource disparities between countries, and the search for a balance between decentralization and the need for standardization to guarantee that the project produces reference genomes of the highest quality possible.

Reference article:

Cartney A M Mc, Formenti G, Mouton A, (...) Fernandez R, (...) Mazzoni C J, et. al. (2024) “The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics”; npj Biodiversity.  DOI: 10.1038/s44185-024-00054-6.