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bioRxiv · 10.1101/2025.11.20.689645

A chromosome-level genome assembly of the South African indigenous, Kolbroek pig, Sus scrofa domesticus

Smith, R. M.·Molotsi, A. H.·Nesengani, L. T.·Tshilate, T. S.·Mdyogolo, S.·Hlongwane, N. L.·Masebe, T. M.·Djikeng, A.·Mapholi, N. O.
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Abstract

The Kolbroek pig is indigenous to South Africa and a breed of choice for smallholder farmers. This is mainly due to its characteristics, such as disease resistance and adaptability to tropical agroecological environments. Despite these desirable traits, the genomic architecture of this breed has not been explored. In this study, we report a high-quality genome assembly of the South African Kolbroek pig sequenced at 31 x coverage through a combination of PacBio Sequel IIe HiFi and Illumina Novaseq 6000 Omni-C sequencing. The assembled genome resulted in a length of 2.6 Gb in size, including 83 Scaffolds, which consist of 19 chromosome-size scaffolds with 138.7 Mb/48.5 Mb for scaffold/contig N50 respectively. The BUSCO completeness at 95.5 %. Genome annotation and structure prediction identified 22,025 genes with protein-coding potential. The genome provides an opportunity to investigate genetic variation across multiple pig breeds and serves as a genetic resource to develop breeding programs for the conservation and improvement of the Kolbroek pig.

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Smith, R. M., Molotsi, A. H., Nesengani, L. T., Tshilate, T. S., Mdyogolo, S., Hlongwane, N. L., Masebe, T. M., Djikeng, A., Mapholi, N. O.. 2025-11-21. A chromosome-level genome assembly of the South African indigenous, Kolbroek pig, Sus scrofa domesticus. https://doi.org/10.1101/2025.11.20.689645

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