Researchers map Saimaa ringed seal genome to aid conservation

Researchers have published a reference genome for the Saimaa ringed seal, providing a highly detailed digital representation of the species’ entire genetic material, Yle reports. The work was carried out by researchers at the University of Eastern Finland and the University of Oulu.

The reference genome can support research into the seals’ adaptation, health and reproduction. It may also help identify genetic causes of pup mortality and guide translocations aimed at preserving the species’ genetic diversity.

A genome contains all of a species’ inherited information, including information about how an individual develops as an embryo and how its physiology, behaviour and appearance are formed. Until now, information about the Saimaa ringed seal’s genome had been fragmented.

Professor Jaakko Pohjoismäki compared the previous situation with the works of Finnish author Kalle Päätalo.

“You could think that Päätalo’s entire body of work exists physically somewhere, but we have only received separate pages from it. We have not known which books they belong to or what context they are part of,” Pohjoismäki said.

A reference genome is a complete, high-quality digital representation of the genome. Pohjoismäki said it was now possible to search the “books” digitally and find, for example, how many times and on which page a particular subject was mentioned.

The Saimaa ringed seal reference genome contains 17 chromosomes and 2.4 billion base pairs, including 21,800 genes. Only a small fraction of the billions of base pairs contain genes, which hold important information. Identifying them had previously been laborious.

Artificial intelligence helped speed up the work. The researchers used an AI tool published this year that identified all 21,800 of the seal’s genes in 45 minutes. The research team then verified the tool’s findings.

The reference genome can be examined and analysed through international genomic databases. It can also be compared with reference genomes from other species, allowing researchers to study how specific genes differ and whether those differences help explain differences in species’ biology.

The genome will complement existing conservation measures, including tissue banking and genomic monitoring. It is also an important part of a newly launched LIFE project that aims to increase the number of seals in Lake Saimaa.

The research team has made an initial assessment of how the reference genome could be used in practice and in conservation work.

“We can study whether there are genetic factors that explain, for example, pup mortality. If there are, we can consider what might be done about it,” Pohjoismäki said.

The species’ limited population threatens its genetic diversity by increasing the risk of inbreeding. Saimaa ringed seals have been moved within Saimaa to preserve as broad a gene pool as possible. The reference genome could help researchers determine where individual seals should be moved and assess how successful the translocations have been.

The DNA used in the study came from a male Saimaa ringed seal named Tuukka, one of three seals translocated in 2023. A skin sample was taken from Tuukka at the time, providing a cell line for obtaining high-quality DNA.

Reference genomes are usually based on samples taken from dead animals. Tuukka is therefore a scientifically unusual case and, in the researchers’ words, something of a genomic ambassador.

“I am a fan of our Tuukka. It feels quite intimate to know its genome so precisely while also knowing that it is still swimming somewhere in Saimaa today,” Pohjoismäki said.