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The Earth BioGenome Project Norway – a national “dugnad”

Kjetill S Jakobsen

Centre for Ecological and Evolutionary Synthesis (CEES)

Univ of Oslo

Norwegian Biodiversity & Genomics Conference 2023

Feb 9 2023

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Sequencing all eukaryotic species on earth

“The EARTH BIOGENOME

PROJECT”

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  • A Norwegian initiative to sequence all species in Norway
  • MOU signed with EBP and UiO March 2019
  • MOU signed between all Norwegian institutions (April-May 2019)
  • White paper EBP-Nor (June 2020)
  • Application submitted to RCN (Oct 2020)
  • Funded from Aug 2021

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NORWAY

EBP-Nor

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The Norwegian EBP initiative

(EBP-Nor)

  • Planned in 3 phases

Funded by the Research Council of Norway

    • Phase 1 2021-2024 (3 million Euro)
    • Planned 150 species
    • Norwegian and arctic species
    • Marine species
    • Coordination with ERGA EBP, VGP, DToL etc.

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  • Preparation for 2 phase has begun
    • New members of the EBP-Nor consortium: UiA, NIVA
    • Recruiting consortium and reference group members

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https://www.ebpnor.org

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European Reference Genome Atlas

https://www.erga-biodiversity.eu/

ERGA is the pan-European partner

of the Earth Biogenome Project (EBP)

  • Pan-European application

to Horizon Europe (Oct

2021; 20 M Euro)

  • BioGenome Europe

Funded (from Sept 2022)

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BioGenome Europe (BGE)

    • Coll. with Uppsala on sequencing
    • Coordination of sampling
    • Selection of species
    • National History Museum,

CEES, UiO involved

    • Barcoding; NorBOL, BIOSCAN

NTNU

European Reference Genome Atlas

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EBP-Nor reference genome standards

  • PacBio HiFi (circular consensus – 99.9% accuracy)
  • HiC (scaffolding)
  • Allows chromosome length assemblies
  • EBP quality measures: N50 contig >1Mb, >90% complete BUSCO genes, >90% of sequence in chromosomes, > less than 1 error per 10000 bp

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Recent improvements

  • Oxford Nanopore: improved chemistry and base calling
    • No need to do Illumina polishing (?)
  • PacBio Revio: faster, reduced costs, more accurate (in order)
    • Avoid HiC scaffolding (?)

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The first EBP-Nor genomes are finished��Update: 65 genomes are curated or underway

Brook lamprey (Lampreta planeri)

River lamprey (Lampreta fluvatilis)

31 fungal species

5 moss species (Sphagnum)

Svalbard reindeer (Rangifer tarandus plathyrynhcus)

Snowy owl (Bubo scandiacus)

Underway: insects (bumble bee, lacewing), Atlantic puffin, cod and salmon (improved), bird cherry (Prunus padus), cloudberry ++

Morterella hyalina

Absida galuca

Basidiomycota

Mucor plumbeus (2 strains)

Mucoromycota

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Prunus padus

(hegg, bird cherry)

Lacewing (Chrysoptidae, gulløye)

(bluethroat, blåstrupe)

(white-throated dipper, fossekall)

  • Invertebrate and algal species are underway
  • 25 additional species sampled/DNA
  • All species “planned/underway”, in progress and curated

can be found at GoaT (https://goat.genomehubs.org)

Cinclus cinclus

Luscinia svecica

Calluna vulgaris

Common heather, ling, røsslyng)

(Cloudberry, molte)

Rubus chamaemourus

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Acknowledgements

  • The CEES EBP-Nor Team, The Norwegian Sequencing Centre
  • NMBU – CIGENE scientists, ON Sequencing, sampling NMBU scientists
  • UiB – core participants, Elixir, sampling UiB scientists
  • NTNU – core participants, sampling NTNU and NINA scientists
  • Uni Nord – core participants
  • UIT – core participants, Elixir, sampling UiT scientists
  • SINTEF – core participants

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