Extensive copy-number variation of young genes across stickleback populations.
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, complexit...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-12-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC4256280?pdf=render |
| _version_ | 1811334839838703616 |
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| author | Frédéric J J Chain Philine G D Feulner Mahesh Panchal Christophe Eizaguirre Irene E Samonte Martin Kalbe Tobias L Lenz Monika Stoll Erich Bornberg-Bauer Manfred Milinski Thorsten B H Reusch |
| author_facet | Frédéric J J Chain Philine G D Feulner Mahesh Panchal Christophe Eizaguirre Irene E Samonte Martin Kalbe Tobias L Lenz Monika Stoll Erich Bornberg-Bauer Manfred Milinski Thorsten B H Reusch |
| author_sort | Frédéric J J Chain |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T17:15:08Z |
| format | Article |
| id | doaj.art-ee391eb0aa684fc0a6c0cca6eaf5d22b |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-13T17:15:08Z |
| publishDate | 2014-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-ee391eb0aa684fc0a6c0cca6eaf5d22b2022-12-22T02:38:10ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042014-12-011012e100483010.1371/journal.pgen.1004830Extensive copy-number variation of young genes across stickleback populations.Frédéric J J ChainPhiline G D FeulnerMahesh PanchalChristophe EizaguirreIrene E SamonteMartin KalbeTobias L LenzMonika StollErich Bornberg-BauerManfred MilinskiThorsten B H ReuschDuplicate 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.http://europepmc.org/articles/PMC4256280?pdf=render |
| spellingShingle | Frédéric J J Chain Philine G D Feulner Mahesh Panchal Christophe Eizaguirre Irene E Samonte Martin Kalbe Tobias L Lenz Monika Stoll Erich Bornberg-Bauer Manfred Milinski Thorsten B H Reusch Extensive copy-number variation of young genes across stickleback populations. PLoS Genetics |
| title | Extensive copy-number variation of young genes across stickleback populations. |
| title_full | Extensive copy-number variation of young genes across stickleback populations. |
| title_fullStr | Extensive copy-number variation of young genes across stickleback populations. |
| title_full_unstemmed | Extensive copy-number variation of young genes across stickleback populations. |
| title_short | Extensive copy-number variation of young genes across stickleback populations. |
| title_sort | extensive copy number variation of young genes across stickleback populations |
| url | http://europepmc.org/articles/PMC4256280?pdf=render |
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