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  Genome-wide genotype-expression relationships reveal both copy number and single nucleotide differentiation contribute to differential gene expression between stickleback ecotypes

Huang, Y., Feulner, P. G. D., Eizaguirre, C., Lenz, T. L., Bornberg-Bauer, E., Milinski, M., et al. (2019). Genome-wide genotype-expression relationships reveal both copy number and single nucleotide differentiation contribute to differential gene expression between stickleback ecotypes. Genome Biology and Evolution, 11(8), 2344-2359. doi:10.1093/gbe/evz148.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-C199-5 Version Permalink: http://hdl.handle.net/21.11116/0000-0004-E9BD-1
Genre: Journal Article

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 Creators:
Huang, Yun1, Author              
Feulner, Philine G D, Author
Eizaguirre, Christophe1, Author              
Lenz, Tobias L.1, Author              
Bornberg-Bauer, Erich, Author
Milinski, Manfred1, 2, Author              
Reusch, Thorsten B H, Author
Chain, Frédéric J J, Author
Affiliations:
1Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445634              
2Emeritus Group Milinski, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2591693              

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 Abstract: Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.

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Language(s): eng - English
 Dates: 2019-07-102019-07-122019-08
 Publication Status: Published in print
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 Identifiers: DOI: 10.1093/gbe/evz148
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Title: Genome Biology and Evolution
  Other : GBE
  Abbreviation : Genome Biol Evol
Source Genre: Journal
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Publ. Info: Oxford : Oxford Univ. Press
Pages: - Volume / Issue: 11 (8) Sequence Number: - Start / End Page: 2344 - 2359 Identifier: ISSN: 1759-6653
CoNE: https://pure.mpg.de/cone/journals/resource/1759-6653