Research project brings together 33 countries to sequence the genome of European species

A new project led by the European Reference Genome Atlas, the European node of the global Earth BioGenome Project (EBP) has brought together a group of researchers and institutions across 33 countries to produce high-quality reference genomes of 98 European species. Institutes of the National Spanish Research Council (CSIC) have played a key role as the genomic node of this pilot project, participating in setting the highest standards for genome sequencing in the species studied, both vertebrates and invertebrates. Researchers from the Institute of Evolutionary Biology (IBE, CSIC-UPF), the Spanish National Science Museum (MNCN-CSIC), the Do?ana Biological Station (EBD-CSIC) and the Botanical Institute of Barcelona (IBB-CSIC), as well as the Spanish National Centre for Genomic Analysis (CNAG) and the Barcelona Computing Center (BSC) among others, have taken part in this project.

The initiative aims at creating a high-quality reference genome database for all the animals, plants, and fungi. 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 and Aristotle’s catfish were sampled by local researchers in Greece to produce genomes that are now openly available for anyone across the world to access and study.

“The Pilot Project has highlighted key challenges, positioning ERGA as a model for decentralised, inclusive, and equitable biodiversity genomics initiatives around the world”, as reported in a new collection of research articles published today in the journal NPJ Biodiversity.

One of the biggest challenges facing the consortium was to establish a quality standard for DNA extraction and processing for all species in the project that would allow the highest quality sequencing and data analysis and that could be shared within the scientific community. Rosa Fernández, principal investigator at IBE, and currently a member of the ERGA executive committee, has been involved in setting this standard, raising the quality of the genomes to chromosome-level precision.

So far, many genomics efforts have employed techniques such as Illumina, PacBio or Nanopore, which are capable of analysing short or long DNA sequences that must then be assembled to reconstruct the genome of the species under study. But this is not enough to have a genome of the highest quality. The IBE team has taken a step forward by employing the novel Hi-C technique, which allows the sequencing of complete chromosomes and the reconstruction of the three-dimensional structure of the genome, optimising protocols for non-model species that are complicated to process in the laboratory.

‘The genome is packed like a ball inside the cell nucleus. With this new technique we are able to unravel and read the ball chromosome by chromosome. In addition, we preserve the folding 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 IBE, led by Judit Salces-Ortiz and Nuria Escudero as key players in the optimisation of the protocols, participated in the sequencing of more than 14 genomes in the pilot project, accompanying several European groups in the fine-tuning of the technique, both in vertebrate and invertebrate species.

The project emphasises equity and inclusiveness, with the aim of making research and genomic resources accessible regardless of geographical boundaries. For many of the participating countries and researchers, the project has been the first opportunity to actively participate in the generation of state-of-the-art reference genomic resources to analyse local native biodiversity.

‘The programme has allowed us to establish a network of infrastructures and collaborations between research groups to generate high quality genomes that is allowing us to more easily tackle the sequencing of new genomes,’ emphasises Maria José Ruiz , CSIC researcher at the EBD. This scientist is a member of the ERGA data analysis committee, which aims to improve the development of genomics applications, establish standard data analysis protocols for different taxonomic groups and promote collaboration and knowledge sharing in genomic data analysis.

European effort with global impact

The ERGA pilot project has also succeeded in generating visibility for the growing importance of biodiversity genomics in Europe and beyond. 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 of the North Atlantic. This new reference genome will allow scientists to make more accurate assessments of the genetic status of the species' stocks, which will ultimately guide 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 Europe-wide collaborative network within ERGA project accelerates scientific progress and facilitates its translation into tangible benefits for biodiversity,’ says MNCN researcher Ana Riesgo, who coordinates the project in Spain with Brent Emerson and Rosa Fernández. ‘In addition, the network helps researchers at all stages of their career to find and share training, collaboration and funding opportunities,’ she continues.

‘This project is also important because access is equitable. One of the objectives was to generate a Europe-wide network that was as inclusive as possible and involved countries where resources for genomic studies are usually limited. And this has been achieved, making access affordable for everyone,’ concludes Ruiz.

ERGA, part of the BioGenome of the Earth project (EBP)

ERGA is the European node of the Earth BioGenome Project (EBP). To achieve its goal of sequencing all eukaryotic life on Earth, the EBP needs global participation and new decentralised models of genome production.?

The ERGA pilot project has demonstrated 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 available. In fact, most of the project's budget came from the efforts of individual members and partner institutions, with additional support from sequencing partners and commercial sequencing companies that provided various contributions.

The initiative has also helped to identify and address the many challenges involved in working on an international scale. These challenges include the legal and logistical hurdles of shipping biological samples across borders, resource disparities between countries, and balancing decentralisation with the need for standardisation to ensure that the project produces reference genomes of the highest possible quality.

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