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

Abstract

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.

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

“…It is believed that animals have been intensively under natural selection for several generations due to fatal AMDV infection. Our study prepared the first map of signatures of selection for response to ADMV infection at the chromosome level using WGS data and based on the new gene annotation after the release of the American mink genome assembly at the chromosomal level by Karimi et al 51 . WGS data has already been used to detect selection signals in other domesticated animals, such as pigs 52 and sheep 53 .…”

Genome-wide association studies for economically important traits in mink using copy number variation

“…The GC content around each SNP marker is known to affect the signal strength through the potential interference of genomic waves 36 . Therefore, we first estimated the percentage of GC content of 1-Mb genomic regions surrounding each marker (500 kb on each side) using faToTwoBit and hgGcPercent tools provided by UCSC Genome Browser 37 and the FASTA information of the American mink genome assembly 1 . Next, the GC content file was implemented in PennCNV by ‘-gcmodel’ function, which applies a regression model for adjusting the high GC content and recovers samples affected by genomic waves 38 .…”

“…The list of genes in the latest American mink reference genome (ASM_NN_V1) 1 was downloaded from the NCBI and the ‘intersect’ function in Bedtools 45 was used to detect the genes that overlapped with significant CNV regions. Finally, an extensive review of the literature was performed to investigate the biological function of identified candidate genes.…”

“…American mink ( Neogale vison ) is one of the most important animals in the global fur industry, yet requires highly efficient breeding programs to deal with challenges faced in mink production systems 1 . Several studies have been carried out to discern the genetics of complex traits affecting the sustainability of mink production, including growth 2 , 3 , feed efficiency 4 , 5 , disease resistance 6 – 9 , pelt quality 10 – 12 , and reproduction traits 13 – 15 .…”

“…The availability of a high-quality chromosome-based genome assembly 1 and a genome-wide SNP array for American mink facilitates the identification of genetic variations underlying economically important traits. Recently, Davoudi et al 4 characterized the CNVs in American mink using whole-genome sequencing data.…”