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A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest

Powell, Daniel LU ; Groβe-Wilde, Ewald ; Krokene, Paal ; Roy, Amit ; Chakraborty, Amrita ; Löfstedt, Christer LU ; Vogel, Heiko ; Andersson, Martin N. LU and Schlyter, Fredrik (2021) In Communications Biology 4.
Abstract

Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy >100 million m3 of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N50 of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome... (More)

Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy >100 million m3 of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N50 of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome sequence from the genus Ips provides timely resources to address questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. In forests of today, increasingly stressed by global warming, this draft genome may assist in developing pest control strategies to mitigate outbreaks.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Communications Biology
volume
4
article number
1059
pages
9 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:85114686473
  • pmid:34504275
ISSN
2399-3642
DOI
10.1038/s42003-021-02602-3
project
The Max Planck Center on next Generation Insect Chemical Ecology
language
English
LU publication?
yes
additional info
Funding Information: We would like to acknowledge the support of the National Genomics Infrastructure (NGI)/ Uppsala Genome Center and UPPMAX for providing assistance in massive parallel sequencing and computational infrastructure. Work performed at NGI / Uppsala Genome Center has been funded by RFI/VR and Science for Life Laboratory, Sweden. We thank several colleagues for discussions and help on genome sizes, chromosomes, and long contigs data: J. Spencer Johnston (Texas A&M University, College Station), Anthony I. Cognato (Michigan State University, East Lansing), and Krystyna Nadachowska-Brzyska & Piotr Zieliński (Jagiellonian University, Krakow). Dr Jan Bílý (Czech University of Life Sciences, Prague) is acknowledged for technical support during RNA samples preparation for tissue transcriptome study. Infrastructural support and salary for A.R., E.G-W. and F.S. were obtained from project EXTEMIT-K CZ.02.1.01/0.0/0.0/15_003/0000433 financed by OP RDE at Czech University of Life Sciences, Prague. M.N.A. was funded by the Swedish Research Council FORMAS (grants #217-2014-689 and #2018-01444). C.L. acknowledges support from the Swedish Research Council VR (grant #2017-03804). P.K. was funded by the Research Council of Norway (grant #249958/F20). Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.
id
49a2aac7-0133-4cc6-bf9f-0a845b77b058
date added to LUP
2021-10-01 10:07:54
date last changed
2024-04-20 12:06:29
@article{49a2aac7-0133-4cc6-bf9f-0a845b77b058,
  abstract     = {{<p>Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy &gt;100 million m<sup>3</sup> of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N<sub>50</sub> of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome sequence from the genus <i>Ips</i> provides timely resources to address questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. In forests of today, increasingly stressed by global warming, this draft genome may assist in developing pest control strategies to mitigate outbreaks.</p>}},
  author       = {{Powell, Daniel and Groβe-Wilde, Ewald and Krokene, Paal and Roy, Amit and Chakraborty, Amrita and Löfstedt, Christer and Vogel, Heiko and Andersson, Martin N. and Schlyter, Fredrik}},
  issn         = {{2399-3642}},
  language     = {{eng}},
  month        = {{09}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Communications Biology}},
  title        = {{A highly-contiguous genome assembly of the Eurasian spruce bark beetle, <i>Ips</i> typographus, provides insight into a major forest pest}},
  url          = {{http://dx.doi.org/10.1038/s42003-021-02602-3}},
  doi          = {{10.1038/s42003-021-02602-3}},
  volume       = {{4}},
  year         = {{2021}},
}