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  Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions

Pezer, Ž., Harr, B., Teschke, M., Babiker, H., & Tautz, D. (2015). Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions. Genome Research, 25(8), 1114-1124. doi:10.1101/gr.187187.114.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-1257-A Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-464F-1
Genre: Journal Article

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Pezer, Željka, Author
Harr, Bettina1, Author              
Teschke, Meike1, Author              
Babiker, Hiba1, Author              
Tautz, Diethard1, Author              
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1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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 Abstract: Copy number variation represents a major source of genetic divergence, yet the evolutionary dynamics of genic copy number variation in natural populations during differentiation and adaptation remain unclear. We applied a read depth approach to genome resequencing data to detect copy number variants (CNVs) ≥1 kb in wild-caught mice belonging to four populations of Mus musculus domesticus. We complemented the bioinformatics analyses with experimental validation using droplet digital PCR. The specific focus of our analysis is CNVs that include complete genes, as these CNVs could be expected to contribute most directly to evolutionary divergence. In total, 1863 transcription units appear to be completely encompassed within CNVs in at least one individual when compared to the reference assembly. Further, 179 of these CNVs show population-specific copy number differences, and 325 are subject to complete deletion in multiple individuals. Among the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns that suggest involvement in local adaptations. We found that genes that overlap with large segmental duplications are generally more copy-number variable. These genes encode proteins that are relevant for environmental and behavioral interactions, such as vomeronasal and olfactory receptors, as well as major urinary proteins and several proteins of unknown function. The overall analysis shows that genic CNVs contribute more to population differentiation in mice than in humans and may promote and speed up population divergence.

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Language(s): eng - English
 Dates: 2015-07-062015-08
 Publication Status: Published in print
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 Identifiers: DOI: 10.1101/gr.187187.114
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Title: Genome Research
Source Genre: Journal
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Publ. Info: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 25 (8) Sequence Number: - Start / End Page: 1114 - 1124 Identifier: ISSN: 1088-9051 (print)
ISSN: 1054-9803 (print)
ISSN: 1549-5469 (online)
CoNE: /journals/resource/954926997202