European genomics initiative to map biodiversity
28 september 2022
Uppsala University and SciLifeLab are participating in a major new EU-funded consortium: Biodiversity Genomics Europe, which involves using genomic methods to study the impact of humans on biodiversity. The initiative brings together European expertise with the aim of producing better tools for preserving biodiversity.
According to experts, one in four existing species is threatened with extinction today, resulting in serious impacts on water and food supplies, ecological cycles and conditions for human life. The consequences of reduced biodiversity are extremely difficult to predict, as there is a lack of important expertise on life on Earth and these species. Despite 300 years of biological systematics, it is estimated that 80 percent of the Earth’s species remain to be described. This situation is further complicated by the fact that all of these species interact with each other, which has an impact on the known species and leads to an incredibly complex web with implications right up to planetary level.
Genomics provides vital tools for filling in knowledge gaps, and the mobilisation now taking place represents a major step forward for this field of research across the continent. The Biodiversity Genomics Europé (BGE) consortium brings together European expertise in two critical areas – genome sequencing and DNA barcoding – and has two aims. Firstly, to map European species diversity using genetic methods (known as barcoding), and secondly to sequence entire genomes from as many European species as possible. Swedish researchers are participating in both projects through Uppsala University and SciLifeLab, which have prominent roles in the production of reference genomes and in how these can be used practically in nature conservation research.
SciLifeLab and its sequencing and bioinformatics platforms have played a key role in Swedish research in recent years, and it will now also play an important role in this consortium.
“Through BGE we will be able to convey our knowledge to the rest of Europe and form a long-term collaborative network. This will enable us to consolidate our leading position in international genomics research,” explains Olga Vinnere Pettersson (SciLifeLab), who is leading one of BGE’s sub-projects.
Practical natural conservation
Among the participating researchers from Uppsala University are Jacob Höglund, Professor of Animal Ecology, and Leif Andersson, Professor of Comparative Genetics and Functional Genomics.
“Mapping diversity and sequencing reference genomes are the foundation of the initiative, but knowledge also needs to be translated into practice. Uppsala University is involved in sequencing high-quality reference genomes as well as in producing methods and working practices for using knowledge in the field of practical natural conservation,” explains Höglund.
“We are responsible for one of the sub-studies conveying the societal benefit of this project. We will carry out detailed genetic mapping of different populations of mackerel and coalfish, with the long-term goal of contributing knowledge that can be used for sustainable fishing of these species,” explains Andersson.
DNA barcoding uses short DNA fragments to distinguish between species, just like barcodes in a shop distinguish between different products. Modern sequencing technology enables DNA barcoding to be used widely and thus radically increases the pace at which new species can be categorised. A basis can then be established for understanding ecological interactions.
Genome sequencing takes place at the other end of the spectrum and aims to establish the entire genetic material of species, which can provide a map of the code that creates organisms. Using this information, researchers can estimate the genetic potential of a species and localise genes and other genomic elements. This type of comprehensive picture can enable modelling of how an organism functions and predict how it will react to changes in the environment.
The EU’s biodiversity strategy for 2030 and the ‘European Green Deal’ reinforce the importance of addressing challenges such as pollinator decline, habitat destruction and the impact of invasive species on established ecosystems. The BGE consortium – funded by the EU’s ‘Horizons programme’ – represents a major investment and the tool that will realise this ambition. BGE will also collaborate with other major international initiatives such as the ‘Earth BioGenome Project’ and ‘International Barcode of Life’.