Researchers at the University of Eastern Finland and the University of Oulu have produced the first chromosome-level reference genome for the Saimaa ringed seal. The sequence of every chromosome in the seal’s entire genome has now been read and assembled into virtual maps, including its gene content. The newly published genome provides a unique perspective on the species’ genetic makeup and adaptation to its freshwater environment. It also supports evidence-based conservation.
A reference genome is a model – as the name suggests, a point of comparison against which genomic data from other individuals can be analysed. It is a carefully assembled representation of what the genome of a species typically looks like, how it is organised into chromosomes, the order of its DNA sequences, and which genes it contains.
“Reference genomes are like maps of a species’ genetic information,” explains Professor Jaakko Pohjoismäki from the University of Eastern Finland.
“A map is only a representation of the terrain, but it still helps us navigate. In the same way, a reference genome helps researchers understand where different genes are located and how individuals differ from one another genetically. Detailed information about genes can also reveal functional differences between species.”
A genome from a living ambassador of the species
Unlike most reference genomes, the newly published genome comes from a living Saimaa ringed seal. The male seal Tuukka was captured in 2023 as part of genetic translocations aimed at safeguarding the remaining genetic diversity of the population. A small skin sample was collected from Tuukka, from which a cell line was established in the laboratory. This provided high-quality DNA with the precision required to determine the sequence of the genome.
The cell line preserves Tuukka’s unique genetic makeup in living form, benefiting not only current research and conservation efforts but also future generations of researchers.
The Saimaa ringed seal genome is 2.35 billion base pairs long and consists of 17 chromosomes, including the sex chromosomes. It contains approximately 21,800 genes, slightly more than the human genome. Genomic comparisons revealed several genetic differences that may be associated with adaptation to a freshwater environment. Examples include genes involved in ion transport and kidney function, which are important for maintaining salt and water balance in freshwater. Differences in olfactory receptors between the species may also reflect adaptation to the environmental conditions of Lake Saimaa.
The Saimaa ringed seal reference genome provides tools for research and conservation
In addition to providing evolutionary insights, the new genome has immediate practical applications. It provides a high-quality reference for studying genetic diversity, inbreeding and population history in the Saimaa ringed seal, as well as for developing monitoring methods. This information is particularly valuable because conservation efforts aim to maintain genetic variation in the small and fragmented seal population.
“A reference genome is an essential resource for developing genetic monitoring tools, not only for identifying individuals and their relationships, but also for monitoring the genetic diversity of the population and inherited defects,” says Associate Professor Stefan Prost from the University of Oulu.
The reference genome will complement ongoing conservation initiatives, including tissue biobanking and genomic monitoring, and will facilitate future studies of adaptation, health, reproduction, and disease in the Saimaa ringed seal.
It will also play a central role in the LIFE project launched in August 2026 (New Milestone in Saimaa Ringed Seal Conservation: Target Population of 700 Individuals by 2032 | Metsähallitus), where it is being used to develop genome-based monitoring tools and investigate the causes of pup mortality. The work also forms a part of the current broader international efforts to generate high-quality reference genomes for Earth’s biodiversity.
The genome is publicly available and can be accessed and analysed through international genomic databases:
https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_059488705.1/ https://www.ebi.ac.uk/ena/browser/view/GCA_059488705.1