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A chromosome-level genome assembly of the Korean minipig (Sus scrofa) - PubMed

️Mon Jan 01 2024

A chromosome-level genome assembly of the Korean minipig (Sus scrofa)

Suyeon Wy et al. Sci Data. 2024.

Abstract

Recent advancements in sequencing and genome assembly technologies have led to rapid generation of high-quality genome assemblies for various species and breeds. Despite the importance as minipigs an animal model in biomedical research, the construction of high-quality genome assemblies of minipigs still lags behind other pig breeds. To address this problem, we constructed a high-quality chromosome-level genome assembly of the Korean minipig (KMP) utilizing multiple different types of sequencing reads and reference genomes. The KMP assembly included 19 chromosome-level sequences with a total length of 2.52 Gb and N50 of 137 Mb. Comparative analyses with the pig reference genome (Sscrofa11.1) demonstrated comparable contiguity and completeness of the KMP assembly. Additionally, genome annotation analyses identified 22,666 protein-coding genes and repetitive elements occupying 40.10% of the genome. The KMP assembly and genome annotation provide valuable resources that can contribute to various future research on minipig and other pig breeds.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1. Chromosome-level genome assembly of the Korean minipig (KMP).**
(a) Workflow for constructing the KMP assembly. (b) A Hi-C contact map of the KMP assembly (Resolution: 5 Mb; MAPQ > 30). (c) Syntenic relationships between the KMP and the pig reference genome assembly (Sscrofa11.1). Ribbons represent correspondence between chromosomes in the two genomes (Resolution: 300 Kb). (d) QV scores of 19 chromosome-level scaffolds in the KMP assembly. (e) Rates of short reads mapped to the KMP and the pig reference genome assembly (**p < 0.0002, *p < 0.02; Mann-Whitney U test).

**Fig. 2. Genome annotation of the KMP assembly.**
(a) Workflow for annotating protein-coding and non-coding genes. (b) Genomic distributions of protein-coding genes and transcripts in chromosome-level scaffolds of the KMP and the pig reference genome assembly (Sscrofa11.1). (c) Sequence divergence of repetitive elements in the KMP assembly.

**Fig. 3. Physical coverages of short reads in breakpoint regions of the KMP assembly.**
(a) Syntenic relationship of chromosome 6 between the KMP and the pig reference genome assembly. Ribbons represent syntenic regions and colored ribbons highlight synteny blocks associated with inversion events. Arrows indicate the five breakpoint regions detected in chromosome 6. (b) Read coverage patterns of short (paired-end and mate-pair) and long reads in breakpoint regions. Colored boxes and dots represent breakpoint regions and read coverages in the boundaries of the breakpoint regions, respectively. Each breakpoint region is indicated by an arrow with the same color as in (a).

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A chromosome-level genome assembly of the Korean minipig (Sus scrofa) - PubMed