Extensive Copy-Number Variation of Young Genes across Stickleback Populations

Chain, Frédéric J. J.; Feulner, Philine; Panchal, Mahesh; Eizaguirre, Christophe; Samonte, Irene E.; Kalbe, Martin; Lenz, Tobias L.; Stoll, Monika; Bornberg-Bauer, Erich; Milinski, Manfred; Reusch, Thorsten B. H.; Zhang, Jianzhi (2014). Extensive Copy-Number Variation of Young Genes across Stickleback Populations. PLoS genetics, 10(12), e1004830. Public Library of Science 10.1371/journal.pgen.1004830

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Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)
08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE) > Aquatic Ecology

UniBE Contributor:

Feulner, Philine

Subjects:

500 Science > 570 Life sciences; biology

ISSN:

1553-7390

Publisher:

Public Library of Science

Language:

English

Submitter:

Marcel Häsler

Date Deposited:

20 Jul 2015 15:35

Last Modified:

23 Feb 2016 08:31

Publisher DOI:

10.1371/journal.pgen.1004830

PubMed ID:

25474574

BORIS DOI:

10.7892/boris.70359

URI:

https://boris.unibe.ch/id/eprint/70359

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