Successful conservation genomics pilot sets the stage to sequence European biodiversity

In an effort to protect the diversity of life on our planet amid a changing climate, researchers around the world are creating high quality reference genomes, for many plants, animals, and fungi. These references provide complete maps of all the DNA in those species, information that can provide invaluable insights into species evolution and how to conserve and restore biodiversity. 

Many of these global efforts are coordinated under the Earth BioGenome Project (EBP), a “moonshot” project to sequence all of Earth’s eukaryotic biodiversity. UC Santa Cruz Assistant Research Scientist Ann Mc Cartney is an Executive Council member of the EBP Project and vice-chair of the European Reference Genome Atlas (ERGA), the European node of the EBP. 

Today, this group released reports on a successful pilot effort that brought local scientists together to produce reference genomes for 98 plant and animal species of conservation, bioeconomic, and cultural importance. Their efforts aim to promote an inclusive, decentralized and equitable model for the future of large-scale conservation genomics. Their findings are presented in a new collection of papers published in the fully open access journal npj Biodiversity. 

“The ERGA Pilot Project attempted to scale our efforts to generate high-quality reference genomes across an entire continent,” Mc Cartney said. “An endeavor of such magnitude was 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.”

The ERGA pilot project coordinated a network of scientists across 33 countries in Europe, where there is a stark disparity in the distribution of resources, particularly within the genomics field, between the different regions of the continent. A major goal of the pilot project was to empower all scientists across Europe to participate in collecting and analyzing data from species in their countries, especially given that the continent is home to major biodiversity hotspots such as the River Rioni in Georgia and the Cape Greco National Forest Park in Cyprus. For many involved, this was their first opportunity to actively engage in generating state-of-the art reference genomic resources for their local native biodiversity.

“It was really important for us to come up with a solution that wouldn't just empower already well resourced institutions to take over the sequencing of everything in Europe, but rather build the capacity in less well resourced institutions and countries,” Mc Cartney said. “We didn’t want this to be another instance of helicopter science where scientists go in saying, ‘can we have your samples, but we'll take care of the sequencing, interpretation, and analyses, and we’ll take most all of the credit.’”
 
Each of the 98 species sequenced for the pilot project had an international and transdisciplinary team of experts that were involved and given credit throughout the process of sequencing the DNA and assembling it into a readable, useful genome. Among the project’s milestones are the first complete genomes of several species from Greece, one of Europe’s most biodiverse countries, such as Aristotle’s Catfish and the Cretan wall lizard. 

Genome sequencing methods have greatly improved in the past few years, and the ERGA team held a number of workshops to enable researchers to quickly produce high quality reference genomes. This included training that was directly related to methods, such as how to physically assemble high quality reference genomes. 

Trainings covered many other topics, such as how to make sure samples are obtained legally, how to make sure the data production is inline with the FAIR (findable, accessible, interoperable, and reproducible) and CARE (collective benefit, authority to control, responsibility and ethics) principles, and how to facilitate inclusion within the project for those already overburdened with work at their institutions. Going forward, any scientist across Europe can contribute to ERGA and access the training platform with a wealth of resources for each step of the genome sequencing process.

Along the way, Mc Cartney and the team encountered challenges to facilitating such a widespread collaboration, including language, legal, and logistical barriers. For example, samples need to be shipped on dry ice to preserve their quality for long read sequencing, but in some countries, shipping companies don’t have a service that can accommodate dry ice shipment, so scientists had to be creative and find other solutions. However, they were surprised and excited by their success and the overall willingness of scientists to collaborate, exchange knowledge, and reduce duplicative efforts to sequence the same species. 

This initial effort sets the stage for the scaling up of these efforts as the EBP enters its second phase, in which the goal is to produce 150,000 species reference genomes. While every region across the globe will encounter its own challenges in doing this work, the researchers hope there are lessons from this pilot project that can be useful to scientists worldwide.