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Video Q&A ViewAttendees 1

Plant-Insect Ecosystems

10-Minute Paper

P-IE: Ecology On-Demand Presentations

A highly contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus: Problems, progress and collaborations

On-Demand
On-Demand

    Presenting Author(s)

  • Fredrik Schlyter

    Professor
    Swedish University of Agricultural Sciences & Czech University of Life Sciences
    Lund, Skane Lan, Sweden

    • Co-Author(s)

  • DP

    Dan Powell

    University of the Sunshine Coast
    Sippy Downs, Queensland, Australia

  • EG

    Ewald Grosse-Wilde

    Max Planck Institute for Chemical Ecology
    Jena, Thuringen, Germany

  • HV

    Heiko Vogel

    Max Planck Institute for Chemical Ecology
    Jena, Thuringen, Germany

  • PK

    Paal Krokene

    Norwegian Institute for Bioeconomy Research
    Aas, Akershus, Norway

  • AR

    Amit Roy

    Assistant Professor
    Czech University of Life Sciences
    Prague, Hlavni mesto Praha, Czech Republic

  • AC

    Amrita Chakraborty

    Czech University of Life Sciences
    Prague, Hlavni mesto Praha, Czech Republic

  • KN

    Krystyna Nadachowska-Brzyska

    Jagiellonian University
    Kraków, Malopolskie, Poland

  • MA

    Martin Andersson

    Lund University
    Lund, Skane Lan, Sweden

We created a highly inbred line (sibling-mating single beetle pairs 10 generations) allowing sequencing with Pacific Biosystems technology as the inbreeding reduces heterozygosity, i.e. reduce the amount of natural sequence variation due to allelic variation. The resultant de novo assembly has extraordinary quality, with a total size of ~236 Mb present in 272 contigs (N50 6.6 Mb).Stranded RNA-Seq data from multiple life stages and tissues was aligned to the assembly. State-of-the art software gave “automated” gene model predictions, allowing a comparison to other high-quality beetle genomes. There is a total of 23,933 genes predicted, missing only 38 (2.3%) of the BOSCO insect orthologs. This is comparable with the Asian longhorn beetle (22,035 genes) but more than the new data for Mountain Pine Beetle (males 13,601). The longest contigs suggest whole chromosome arms or full chromosomes.  Genes number for chemosensation, detoxification, and pesticide resistance was similar or higher compared to 11 Coleoptera genomes.

Use of data already include manual annotation for chemosensation genes, de-orphanization of olfactory receptors, insect-tree RNA-Seq transcriptomics, and for gene knockout. In the longer term, the result will be an annotated, very high-quality genome, that useful not only for study of evolution, ecology, and, management in Ips spp, but also for other Ipini and Scolytinae. It will allow for improved studies of functional genomics overall. In today's forests, stressed by global warming, it may ultimately aid in developing novel management strategies mitigating outbreaks.

Published 9 Sept 2021 Communications Biology 4: 1059  10.1038/s42003-021-02602-3