Fig. 1: Chromosome-level genome assembly (NCMD) of the Nanchukmacdon pig breed.

(a) Length distribution of raw Pacbio subreads of Nanchukmacdon. The mean and median subread lengths were 9.90 Kbp (Red line) and 7.57 Kbp (Blue line), respectively. (b) Workflow for the genome assembly of Nanchukmacdon. Grey-colored boxes represent programs, and yellow-, blue-, and red-colored boxes indicate the input and output of the programs for building contigs, reference-guided scaffolding and Hi-C based scaffolding. The box named “References” represents the genome sequences of related species. (c) Comparison results between NCMD and pig reference genome assembly (Sscrofa11.1). Ribbons show the syntenic relations between the two genomes, and bar plots in the outer rings represent the distribution of protein-coding (PCG, colored by red) and non-coding (NCG, colored by blue) genes in each assembly. (d) Heatmap of the Nanchukmacdon Hi-C reads mapped to the NCMD assembly (resolution: 1 Mbp). The Darkness of the red color represents the strength of chromosome interactions. (e) QV scores of chromosomes in the NCMD assembly and the genome assemblies of goat (ARS1)³⁴, cow (ARS-UCD1.2)⁶⁴ and water buffalo (UOA_WB_1)⁶⁵. (f) Comparison of the mapping rates of all reads (“All reads”) and properly mapped reads (“Properly mapped reads”) against the NCMD and pig reference genome assembly (***p < 0.001, Mann-Whitney U test). (g) Comparison of repeat ratios in closed gap regions and other genomic regions of the NCMD and pig reference genome assembly (***p < 0.001, Mann-Whitney U test).