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Novel origins of co...
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Berglund, JonasUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
(author)
Novel origins of copy number variation in the dog genome
- Article/chapterEnglish2012
Publisher, publication year, extent ...
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Springer Science and Business Media LLC,2012
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-194244
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-194244URI
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https://doi.org/10.1186/gb-2012-13-8-r73DOI
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https://res.slu.se/id/publ/42849URI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
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Additional author: The LUPA Consortium (www.eurolupa.org)
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BACKGROUND: Copy number variants (CNVs) account for substantial variation between genomes and are a major source of normal and pathogenic phenotypic differences. The dog is an ideal model to investigate mutational mechanisms that generate CNVs as its genome lacks a functional ortholog of the PRDM9 gene implicated in recombination and CNV formation in humans. Here we comprehensively assay CNVs using high-density array comparative genomic hybridization in 50 dogs from 17 dog breeds and 3 gray wolves. RESULTS: We use a stringent new method to identify a total of 430 high-confidence CNV loci, which range in size from 9 kb to 1.6 Mb and span 26.4 Mb, or 1.08%, of the assayed dog genome, overlapping 413 annotated genes. Of CNVs observed in each breed, 98% are also observed in multiple breeds. CNVs predicted to disrupt gene function are significantly less common than expected by chance. We identify a significant overrepresentation of peaks of GC content, previously shown to be enriched in dog recombination hotspots, in the vicinity of CNV breakpoints. CONCLUSIONS: A number of the CNVs identified by this study are candidates for generating breed-specific phenotypes. Purifying selection seems to be a major factor shaping structural variation in the dog genome, suggesting that many CNVs are deleterious. Localized peaks of GC content appear to be novel sites of CNV formation in the dog genome by non-allelic homologous recombination, potentially activated by the loss of PRDM9. These sequence features may have driven genome instability and chromosomal rearrangements throughout canid evolution.
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Nevalainen, Elisa M
(author)
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Molin, Anna-MajaSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics(Swepub:slu)50053
(author)
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Perloski, Michele
(author)
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André, Catherine
(author)
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Zody, Michael C
(author)
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Sharpe, Ted
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Hitte, Christophe
(author)
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Lindblad-Toh, KerstinUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)kerli865
(author)
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Lohi, Hannes
(author)
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Webster, Matthew TUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)maweb226
(author)
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Andersson, GöranThe LUPA Consortium(Swepub:slu)50422
(author)
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Uppsala universitetInstitutionen för medicinsk biokemi och mikrobiologi
(creator_code:org_t)
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Sveriges lantbruksuniversitet
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In:Genome Biology: Springer Science and Business Media LLC13:8, s. R73-1465-69061474-760X1474-7596
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Molin, Anna-Maja
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Zody, Michael C
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Sharpe, Ted
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Genome Biology
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Uppsala University
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Swedish University of Agricultural Sciences