A near-complete Landrace pig ( Sus scrofa ) genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The Duroc-derived reference genome Sscrofa11.1 has provided a critical foundation for pig genomics, supporting accurate variant detection and comparative analyses, but does not capture breed-specific variation. Here, we present a near-complete genome assembly for the Landrace pig (Landrace_v1, GCA_963921485.1), spanning all 20 chromosomes and totaling 2.6 Gb, including 176 Mb of sequence absent from Sscrofa11.1. Comparative analyses with recently published high-quality pig genomes reveals conserved centromere organization across breeds, accompanied by substantial variation in repeat composition and length, and identifies a pig-specific pattern of telomere variant repeats across eight breeds. The improved resolution of repetitive regions in Landrace_v1 enables more complete reconstruction of complex gene families, including olfactory receptors, and uncovers structural variation at the KIT proto-oncogene receptor tyrosine kinase locus absent from the Duroc reference. Together, these findings highlight limitations of single-reference genomes and demonstrate the value of breed-specific assemblies for capturing genomic diversity and improving downstream analyses.