Genomic copy number variation in Mus musculus

Locke, M Elizabeth O; Milojevic, Maja; Eitutis, Susan T; Patel, Nisha; Wishart, Andrea E; Daley, Mark; Hill, Kathleen A.

doi:10.1186/s12864-015-1713-z

Cited by 41 publications

(47 citation statements)

References 115 publications

(135 reference statements)

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“…On average, ∼140 Mb of the polar bear and brown bear genome are CN-variable, accounting for ∼6% of the reference polar bear genome assembly. These findings are consistent with results observed in other mammals (∼5% in humans, ∼6.9% in mice, and ∼4% in cows) (12,40,41). Because CNV appears so abundant and dynamic within mammalian genomes, we explored the hypothesis that natural selection has acted on this form of genetic variation to facilitate adaptive refinements during polar bear evolution.…”

Section: Discussionsupporting

confidence: 86%

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

Rinker

Specian

Zhao

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.

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Section: Discussionsupporting

confidence: 86%

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

Rinker

Specian

Zhao

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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“…Whether the genes themselves or their regulatory elements are affected by these copy number variants, the functions attributed to the genes align with differences that are consistently reported between marine and freshwater populations: immunity, muscle development, and morphology of the head and limbs. Multiple case studies also implicate adaptive copy number variation in aiding the immunity of humans (Gonzalez et al 2005;Iskow et al 2012) and mice (Locke et al 2015;Pezer et al 2015), supporting the hypothesis that copy number variation is a general mechanism for adaptation of the vertebrate immune system.…”

Section: Discussionmentioning

confidence: 70%

Detecting differential copy number variation between groups of samples

et al. 2017

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We present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use a finite-state transducer where the emitted read depth is conditioned on the mappability and GC-content of all reads that occur at a given base position. In this model, the read depth within a region is a mixture of binomials, which in simulations matches the read depth more closely than the often-used negative binomial distribution. The method analyzes all samples simultaneously, preserving uncertainty as to the breakpoints and magnitude of CNVs present in an individual when it identifies CNVs differentially present between the two groups. We apply this method to identify CNVs that are recurrently associated with postglacial adaptation of marine threespine stickleback () to freshwater. We identify 6664 regions of the stickleback genome, totaling 1.7 Mbp, which show consistent copy number differences between marine and freshwater populations. These deletions and duplications affect both protein-coding genes and -regulatory elements, including a noncoding intronic telencephalon enhancer of The functions of the genes near or included within the 6664 CNVs are enriched for immunity and muscle development, as well as head and limb morphology. Although freshwater stickleback have repeatedly evolved from marine populations, we show that freshwater stickleback also act as reservoirs for ancient ancestral sequences that are highly conserved among distantly related teleosts, but largely missing from marine stickleback due to recent selective sweeps in marine populations.

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“…The CNVR coverage of the genome was similar to results in other species, including mouse (6.87% of the genome; Locke et al . ) and human (12% of the genome; Redon et al . ).…”

Section: Resultsmentioning

confidence: 99%

Genome‐wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds,

2016

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Copy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next-generation sequence data. First, in order to determine a suitable strategy for CNV detection in our data, we compared the performance of three distinct CNV detection algorithms on benchmark CNV datasets and concluded that using the multiple sample read depth approach was the best method for identifying CNVs in our sequences. Using this technique, we identified a total of 1341 copy number variable regions (CNVRs) from genome sequences of 154 purebred sires used in Cycle VII of the USMARC Germplasm Evaluation Project. These bulls represented the seven most popular beef breeds in the United States: Hereford, Charolais, Angus, Red Angus, Simmental, Gelbvieh and Limousin. The CNVRs covered 6.7% of the bovine genome and spanned 2465 protein-coding genes and many known quantitative trait loci (QTL). Genes harbored in the CNVRs were further analyzed to determine their function as well as to find any breed-specific differences that may shed light on breed differences in adaptation, health and production.

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Genomic copy number variation in Mus musculus

Cited by 41 publications

References 115 publications

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift

Detecting differential copy number variation between groups of samples

Genome‐wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds,

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