Sequencing & Pangenomes

A high-quality chromosome-level genome assembly of the Boer goat using PacBio HiFi and Omni-C sequencing

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Abstract

The Boer goats (Capra hircus) are indigenous to South Africa and well known for their quality meat production. They are well adapted to harsh climatic conditions with a rapid growth rate, which makes them a breed of choice for small-scale and commercial farmers. Like many indigenous livestock, their genetic architecture has been understudied. Comprehensive genomic resources are essential to improve the accuracy of genomic selection and functional annotation in the goat industry. The general objective of this study is to generate a high-quality chromosomal-level genome reference of the Boer goat. We collected blood from a pure Boer goat, which was sequenced through PacBio revio for HiFi reads and Nova seq 6000 for Omni-C reads, following the Vertebrate Genomes Project (VGP) workflow in Galaxy. The final genome size spans 2.74 Gb, which is within the expected genome size of the goat with 322 scaffolds and 521 contigs. The assembly has high contiguity with scaffold N50 of 107.3 Mb, contig N50 of 57.77 Mb, and a total gap length of 39.8 kb. The Benchmarking Universal single-copy orthologs (BUSCO) completeness is at 95.4%. This is the first high-quality genome reference of the Boer goat, which represents one of the most contiguous goat assemblies to date and a significant improvement over previous references. This provides an opportunity for a robust foundation for structural variant detection, functional genomics, and the development of improved genomic prediction tools in meat goats, especially the South African indigenous goats. Conversely, this result enhances the resources for genome-enabled breeding strategies and supports comparative analyses across Capra breeds.

Keywords: 2026

How to Cite:

Nesengani, L., Smith, R., Mdyogolo, S., Tshilate, T., Malemela, M. & Mapholi, N., (2026) “A high-quality chromosome-level genome assembly of the Boer goat using PacBio HiFi and Omni-C sequencing”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285437. doi: https://doi.org/10.31274/wcgalp.23707

Rights: 1