Population Genomics of American Mink Using Whole Genome Sequencing Data

Karimi, Karim; Ngoc, Duy; Sargolzaei, Mehdi; Miar, Younes

doi:10.3390/genes12020258

Cited by 11 publications

(37 citation statements)

References 81 publications

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“…American mink ( Neogale vison ) is well-known as one of the most important sources of fur across the world [ 66 ]. It is essential for the mink industry to implement highly efficient breeding plans to meet sustainable production requirements [ 47 ]. Genome-wide identification of CNVs can provide new insights into genomic variations, which can assist in developing genomic breeding strategies for American mink.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Discussionmentioning

confidence: 99%

“…To keep the relationship between individuals low, we checked the pedigree information and selected individuals with the lowest degree of kinship for the further analyses (median = 0.015; 1st–3rd quantile of relatedness = 0.008–0.039). More details were provided about the studied individuals by Karimi et al [ 47 ].…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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“…American mink has been raised in captivity since the middle 19th century owing to having one of the most desirable sources of fur in the world 2 . The increasing cost of fur production and emerging diseases (e.g., Aleutian disease and coronavirus) are the most important challenges affecting the mink industry in recent years 3 . Although the mink industry requires an efficient breeding program to deal with the aforementioned issues 4 , modern breeding strategies have not been broadly developed in this industry.…”

Section: Introductionmentioning

confidence: 99%

“…However, this draft was highly fragmented and consisted of 7175 scaffolds with the N50 of 6.3 Mb. Despite the advances in genome-wide studies of American mink through the availability of this draft, the lack of chromosomal information as well as existing short-length scaffolds led to some restrictions in genomic studies of mink e.g., linkage disequilibrium 17 , population genomics 3 , genome-wide association studies 18 and detection of selection signatures 19 . For instance, the analyses of population genomics 3 and signatures of selection 19 were restricted to scaffolds >10 Mb due to removing small scaffolds.…”

Section: Introductionmentioning

confidence: 99%

“…Despite the advances in genome-wide studies of American mink through the availability of this draft, the lack of chromosomal information as well as existing short-length scaffolds led to some restrictions in genomic studies of mink e.g., linkage disequilibrium 17 , population genomics 3 , genome-wide association studies 18 and detection of selection signatures 19 . For instance, the analyses of population genomics 3 and signatures of selection 19 were restricted to scaffolds >10 Mb due to removing small scaffolds. Consequently, the effective length of genome regions, in which single nucleotide polymorphisms (SNPs) were called, was limited to 802 Mb in the study of homozygous regions across the genome 3 .…”

Section: Introductionmentioning

confidence: 99%

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A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison)

et al. 2022

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Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.

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Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison)

Vahedi,

Salek Ardestani,

Banabazi

et al. 2024

Sci Rep

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Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by Aleutian mink disease virus (AMDV). This study aimed to identify candidate regions and genes underlying selection for response against AMDV using whole-genome sequence (WGS) data. Three case–control selection signatures studies were conducted between animals (N = 85) producing high versus low antibody levels against AMDV, grouped by counter immunoelectrophoresis (CIEP) test and two enzyme-linked immunosorbent assays (ELISA). Within each study, selection signals were detected using fixation index (FST) and nucleotide diversity (θπ ratios), and validated by cross-population extended haplotype homozygosity (XP-EHH) test. Within- and between-studies overlapping results were then evaluated. Within-studies overlapping results indicated novel candidate genes related to immune and cellular responses (e.g., TAP2, RAB32), respiratory system function (e.g., SPEF2, R3HCC1L), and reproduction system function (e.g., HSF2, CFAP206) in other species. Between-studies overlapping results identified three large segments under strong selection pressure, including two on chromosome 1 (chr1:88,770–98,281 kb and chr1:114,133–120,473) and one on chromosome 6 (chr6:37,953–44,279 kb). Within regions with strong signals, we found novel candidate genes involved in immune and cellular responses (e.g., homologous MHC class II genes, ITPR3, VPS52) in other species. Our study brings new insights into candidate regions and genes controlling AD response.

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Population Genomics of American Mink Using Whole Genome Sequencing Data

Cited by 11 publications

References 81 publications

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

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

A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison)

Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison)

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