Genome-wide detection of copy number variation in American mink using whole-genome sequencing

doi:10.1186/s12864-022-08874-1

. 2022 Sep 13;23(1):649.

doi: 10.1186/s12864-022-08874-1.

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

Affiliations

¹ Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
² Department of Pathobiology, University of Guelph, Guelph, ON, Canada.
³ Select Sires Inc., Plain City, OH, USA.
⁴ Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
⁵ Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada. miar@dal.ca.

PMID: 36096727
PMCID: PMC9468235
DOI: 10.1186/s12864-022-08874-1

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

Pourya Davoudi et al. BMC Genomics. 2022.

. 2022 Sep 13;23(1):649.

doi: 10.1186/s12864-022-08874-1.

Authors

Affiliations

¹ Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
² Department of Pathobiology, University of Guelph, Guelph, ON, Canada.
³ Select Sires Inc., Plain City, OH, USA.
⁴ Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
⁵ Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada. miar@dal.ca.

PMID: 36096727
PMCID: PMC9468235
DOI: 10.1186/s12864-022-08874-1

Abstract

Background: Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta.

Results: A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3).

Conclusions: This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.

Keywords: American mink; Copy number variation; Whole-genome sequencing.

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Conflict of interest statement

The authors declare they have no competing interests.

Figures

**Fig. 1**
Numbers of CNVs identified across autosomal chromosomes of American mink

**Fig. 2**
Distribution of CNVR types in American mink

**Fig. 3**
Distribution of CNVR sizes in American mink

**Fig. 4**
Genomic landscape of CNVR in American mink

**Fig. 5**
The top ten significant gene ontology terms enriched in CNVR-harbor genes

**Fig. 6**
The KEGG pathways enriched in CNVR-harbor genes

See this image and copyright information in PMC

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References

1. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 2011;470:59–65. doi: 10.1038/nature09708. - DOI - PMC - PubMed
1. Saitou M, Gokcumen O. An evolutionary perspective on the impact of genomic copy number variation on human health. J Mol Evol. 2020;88:104–119. doi: 10.1007/s00239-019-09911-6. - DOI - PubMed
1. Liu GE, Bickhart DM. Copy number variation in the cattle genome. Funct Integr Genomics. 2012;12:609–624. doi: 10.1007/s10142-012-0289-9. - DOI - PubMed
1. Wang Y, Gu X, Feng C, Song C, Hu X, Li N. A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method. Anim Genet. 2012;43:282–289. doi: 10.1111/j.1365-2052.2011.02308.x. - DOI - PubMed
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[1] Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 2011;470:59–65. doi: 10.1038/nature09708. - DOI - PMC - PubMed

[2] Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 2011;470:59–65. doi: 10.1038/nature09708. - DOI - PMC - PubMed

[3] Saitou M, Gokcumen O. An evolutionary perspective on the impact of genomic copy number variation on human health. J Mol Evol. 2020;88:104–119. doi: 10.1007/s00239-019-09911-6. - DOI - PubMed

[4] Saitou M, Gokcumen O. An evolutionary perspective on the impact of genomic copy number variation on human health. J Mol Evol. 2020;88:104–119. doi: 10.1007/s00239-019-09911-6. - DOI - PubMed

[5] Liu GE, Bickhart DM. Copy number variation in the cattle genome. Funct Integr Genomics. 2012;12:609–624. doi: 10.1007/s10142-012-0289-9. - DOI - PubMed

[6] Liu GE, Bickhart DM. Copy number variation in the cattle genome. Funct Integr Genomics. 2012;12:609–624. doi: 10.1007/s10142-012-0289-9. - DOI - PubMed

[7] Wang Y, Gu X, Feng C, Song C, Hu X, Li N. A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method. Anim Genet. 2012;43:282–289. doi: 10.1111/j.1365-2052.2011.02308.x. - DOI - PubMed

[8] Wang Y, Gu X, Feng C, Song C, Hu X, Li N. A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method. Anim Genet. 2012;43:282–289. doi: 10.1111/j.1365-2052.2011.02308.x. - DOI - PubMed

[9] Bickhart DM, Liu GE. The challenges and importance of structural variation detection in livestock. Front Genet. 2014;5:37. doi: 10.3389/fgene.2014.00037. - DOI - PMC - PubMed

[10] Bickhart DM, Liu GE. The challenges and importance of structural variation detection in livestock. Front Genet. 2014;5:37. doi: 10.3389/fgene.2014.00037. - DOI - PMC - PubMed

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Genome-wide detection of copy number variation in American mink using whole-genome sequencing

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Genome-wide detection of copy number variation in American mink using whole-genome sequencing

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