Copy number variation and population-specific immune genes in the model vertebrate zebrafish

  1. Yannick Schäfer
  2. Katja Palitzsch
  3. Maria Leptin
  4. Andrew R Whiteley
  5. Thomas Wiehe  Is a corresponding author
  6. Jaanus Suurväli  Is a corresponding author
  1. University of Cologne, Germany
  2. University of Montana, United States
  3. University of Manitoba, Canada

Abstract

Copy number variation in large gene families is well characterized for plant resistance genes, but similar studies are rare in animals. The zebrafish (Danio rerio) has hundreds of NLR immune genes, making this species ideal for studying this phenomenon. By sequencing 93 zebrafish from multiple wild and laboratory populations we identified a total of 1,513 NLRs, many more than the previously known 400. Approximately half of those are present in all wild populations, but only 4% were found in 80% or more of the individual fish. Wild fish have up to two times as many NLRs per individual and up to four times as many NLRs per population than laboratory strains. In contrast to the massive variability of gene copies, nucleotide diversity in zebrafish NLR genes is very low: around half of the copies are monomorphic and the remaining ones have very few polymorphisms, likely a signature of purifying selection.

Data availability

NLR reads are available in the NCBI Sequence Read Archive (BioProject PRJNA966920). Scripts are available on GitHub (https://github.com/YSchaefer/pacbio\_zebrafish). Sequences of the hybridization baits are provided as a source dataset.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Yannick Schäfer

    Institute for Genetics, University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Katja Palitzsch

    Institute for Genetics, University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6292-4925
  3. Maria Leptin

    Institute for Genetics, University of Cologne, Cologne, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7097-348X
  4. Andrew R Whiteley

    WA Franke College of Forestry and Conservation, University of Montana, Missoula, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Thomas Wiehe

    Institute for Genetics, University of Cologne, Cologne, Germany
    For correspondence
    twiehe@uni-koeln.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8932-2772
  6. Jaanus Suurväli

    Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
    For correspondence
    jaanus.suurvali@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0133-7011

Funding

Deutsche Forschungsgemeinschaft (SPP1819)

  • Maria Leptin

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Detlef Weigel, Max Planck Institute for Biology Tübingen, Germany

Version history

  1. Received: March 28, 2024
  2. Accepted: June 3, 2024
  3. Accepted Manuscript published: June 4, 2024 (version 1)

Copyright

© 2024, Schäfer et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Yannick Schäfer
  2. Katja Palitzsch
  3. Maria Leptin
  4. Andrew R Whiteley
  5. Thomas Wiehe
  6. Jaanus Suurväli
(2024)
Copy number variation and population-specific immune genes in the model vertebrate zebrafish
eLife 13:e98058.
https://doi.org/10.7554/eLife.98058

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https://doi.org/10.7554/eLife.98058

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