Copy number variation and population-specific immune genes in the model vertebrate zebrafish
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.
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Targeted PacBio Sequencing of Zebrafish NLR ExonsNCBI Bioproject, PRJNA966920.
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Genome assembly GRCz11NCBI Assembly, GCF_000002035.6.
Article and author information
Author details
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
- Detlef Weigel, Max Planck Institute for Biology Tübingen, Germany
Version history
- Received: March 28, 2024
- Accepted: June 3, 2024
- 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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