Earth Biogenome Project collaborations

NAISS 2023/5-307


NAISS Medium Compute

Principal Investigator:

Henrik Lantz


Uppsala universitet

Start Date:


End Date:


Primary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Secondary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)

Tertiary Classification:

10615: Evolutionary Biology




We will be using this project to run genome assembly analyses in two funded projects: VR-EBP and Biodiversity Genomics Europe (BGE). VR-EBP received funding in the 2020 VR-call "Increased accessibility to existing infrastructures". The title of the application was "A Swedish Earth Biogenome Project platform: building a pipeline and proof of principle studies" and is driven by the NBIS and NGI platforms at SciLifeLab together with several researchers in Uppsala and Stockholm. There are also external partners in the project where the efforts of "increased accessibility" are aimed, including SVA and the Swedish Agency for Marine and Water management. The funding is for 4 years, ends at the end of 2024. BGE is a European project funded through a call in Horizon Europe. It consists of two streams of which we are involved in European Reference Genome Atlas (ERGA). We (through Uppsala University and SciLifeLab) are funded to assemble genomes of European species, most of which are threatened or found in Biodiversity hotspots. Runs until the end of 2025. The work will be performed by staff at the NBIS and NGI platforms at SciLifeLab. All of the assembled genomes will also be reported in Earth Biogenome Project and will contribute to the global aim of assembling all eukaryote species on Earth. The data used will be mostly be long read PacBio Hifi data, and Illumina RNA-seq to be used in annotation. Of the species we know we will be receiving, there are several marine worms and mollusks from the Mediterranean area, but also a Swedish beetle (Hydroglyphus hamulatus). In VR-EBP there is also a population genomics component, and we will be working with Swedish samples and use the results to determine population structure and also use them as a basis for decisions in conservation efforts.