The production of reference-quality genomes from non-model organisms at the University of Eastern Finland began with Finnish brown hares, opening the door to European genome research networks.
- Text Marianne Mustonen
- Photos Niko Jouhkimainen and Mikko Suonio, Metsähallitus
In recent years, researchers at the University of Eastern Finland have been both leading and contributing to collaborative genome projects. These efforts have produced reference-quality genome assemblies for the Finnish brown hare and the mountain hare, as well as the Saimaa ringed seal, in collaboration with research partners. Work on the Finnish forest reindeer genome is currently under way. Altogether, the genomes of 20 species have been published through collaborative projects involving UEF researchers.
Genome sequencing would not be possible without the rapid development of sequencing methods.
“Modern bioscientific research is extremely equipment-intensive. With current resources, it is difficult to remain at the forefront of research in many fields. However, services such as DNA sequencing can now be outsourced to commercial providers very cost-effectively,” says Professor Jaakko Pohjoismäki from the Department of Environmental and Biological Sciences at the University of Eastern Finland.
“Today, this is a remarkably level playing field. Research is carried out on an ordinary laptop computer with access to a supercomputer. This means that we do not have to compete over who has the most resources.”
The genomes sequenced by the researchers are included in the European Reference Genome Atlas (ERGA), which aims to map vast numbers of genomes over the coming years. Finland is home to approximately 50,000 species, while Europe as a whole may have as many as 100,000. Samples of rare robber flies and other endangered insects have also been collected for the project in Eastern Finland.
The Darwin Tree of Life project, which is sequencing species found across Britain and Ireland, is the most advanced genome-mapping initiative. Project Psyche, in turn, focuses on sequencing all European butterfly and moth species. The polar admiral is among the species from Eastern Finland included in the project.
“Work on butterfly and moth genomes is progressing rapidly. More than 1,000 genomes have now been sequenced out of a total of 11,000,” Pohjoismäki says.
“Butterflies and moths were selected because their genomes are small and easy to assemble. They are also sympathy-evoking and well-known organisms. One important objective of butterfly and moth research is to determine how genomes change over the course of evolution and how these species adapt to changing conditions such as global warming.”
The life-history strategies of mountain hares and Finnish brown hares differ markedly
The genetic differences between the Finnish brown hare and the mountain hare continue to be studied in a project funded by the Research Council of Finland. The project seeks to understand the species’ life-history strategies.
“Species have a finite amount of energy available, which they can invest either in reproduction or in longevity. The Finnish brown hare reproduces prolifically and grows rapidly, whereas the mountain hare can live for up to 19 years but reproduces more slowly,” Pohjoismäki explains.
The mountain hare and the Finnish brown hare diverged from a common ancestor around three million years ago, evolving distinct adaptations to different environmental conditions and habitats. The mountain hare, for example, thrives in the northern winter conditions, even with scarce or poor-quality nutrition.
“Adaptation may be influenced by differences in metabolism, as reflected in the faster growth of Finnish brown hare cells. Once we know the genomes and gene content of both species, we can identify which genetic differences might underlie this particular trait. Cultured cells can also be used to test experimentally whether a certain gene variant is associated with the studied trait. We can edit a gene and observe how this affects cell growth or a particular metabolic pathway.”
“The mountain hare lives longer and appears to invest more heavily in repairing its genome than the Finnish brown hare. This research could also contribute to the treatment of human diseases as well as to ageing research. Cancer, for example, is a disease in which cells divide uncontrollably. Some species are more susceptible to cancer than others, which is why understanding differences in cell division is important,” he says.
The Finnish forest reindeer genome, meanwhile, is being studied with support from the North Karelia Regional Fund of the Finnish Cultural Foundation. The genome comes from a male calf born at Korkeasaari Zoo in Helsinki. Researchers established a cell line from a small skin sample collected when the calf was ear-tagged.
High-quality cell lines are essential for high-quality research on mammalian genomes.
Jaakko Pohjoismäki
Professor
“We have a Cell Zoo on the Joensuu Campus that includes cell samples from ten Saimaa ringed seals, among others. At least in theory, this provides a way of preserving the genetic diversity of an endangered species in living form.”
“The cells in the Cell Zoo can be reprogrammed into stem cells, opening up future possibilities for supporting reproductive methods as a part of species conservation, although such approaches would require further research. Our biobank can be used for research on a wide range of species in the future. Although cells are relatively simple in terms of their structure and function, they retain species-specific characteristics that can help to understand biological processes and differences that can be highly complex at the organism level.”
Currently, the researchers are particularly interested in the genome and cell lines of the Saimaa ringed seal, as these could shed light on adaptation to aquatic life and the effects of genetic diversity.
“It has been wonderful to see how open and inspiring the European genome research community is. Rather than competing, the community places its trust in collaboration and knowledge sharing,” Pohjoismäki concludes.
