25 January 2023

Building a Danish reference genome sequencing infrastructure


Centre Director Tom Gilbert is thrilled with a new opportunity to build a local reference genome sequencing infrastructure to produce high quality genomes here in Denmark from animals, plants, fungi, and other complex organisms. This new opportunity was made possible by a research infrastructure grant funded by the Carlsberg Foundation.

Credit: Colourbox

Research is often a complex affair. The production of useful research results is influenced by a myriad of factors, and the research process is built up by a lot of different – but often equally important – steps. One essential step for the research being done at Center for Evolutionary Hologenomics (CEH) is having high-quality genome sequences to work with, and as these are not always available, they must be produced. Therefore, Centre Director of CEH Tom Gilbert is thrilled to have gotten the opportunity “to create a facility that researchers based in Denmark, the Farøe Islands and Greenland, can use to generate high quality reference genome sequences for their study species, for use in their ongoing research and to release publicly for the good of science.” 

High-quality genome sequences needed

“As we enter 2023 there are only ca 10,000 distinct eukaryotic species for which we have full genome sequence information, or ca. 1% of the total known. However, of these, fewer than 500 are sequenced to ‘chromosome reference quality’, a standard for contiguity, completeness, and nucleotide base-calling accuracy” says Director of CEH Tom Gilbert. This is an obvious hindrance in the research work of scientists working with genomes. Therefore, the need for available high quality genome sequences is not only characteristic to the centre but to the genomic research world at large. 

Having an infrastructure that enables a systematic, uniform, and high-quality production and keeping of these genome sequences would be a big win for everyone doing genomic research. It would support the continued production of high-value science, and through this – and more importantly – the solution to many of the detrimental problems that the world is facing right now.

The potential solution 

In December 2022, Tom received 2.25 million DKK from the Carlsberg Foundation to create just such an infrastructure. The project takes its starting point in the Earth BioGenome Project (EBP), which “has been launched with the aim of encouraging a global collaboration aimed at sequencing all known eukaryotic biodiversity to the reference quality standards, and in doing so, providing a secure foundation for the future understanding, preservation and mobilisation of the earth’s biosphere to assure planetary and thus human survival” according to Tom. This new Danish reference genome sequencing infrastructure also capitalises on prior investment by the Novo Nordisk Foundation in PacBio sequencing technology with Toms collaborator Prof. Søren Sørensen at UCPH’s Department of Biology. The infrastructure aims at becoming “a major contributor to the goals of the EBP”. This is because Denmark already has the resources needed - the key laboratory as well as computational infrastructure - and now also the funding to hire the needed people to make it all happen. 



Professor and Center Director Tom Gilbert