Sequencing & Pangenomes

High-quality genome assemblies of three Nguni cattle ecotypes using PacBio HiFi and Omni-C sequencing

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Abstract

Nguni cattle are indigenous to Southern Africa and are generally known to be disease resistant, adaptable to harsh climatic conditions. Nguni cattle have diverse ecotypes based on the location they are found in Southern Africa. This breed is commonly used by smallholder farmers and recently also within the commercial sector. This is due to their ability to perform well with minimal inputs. Like many African indigenous cattle, their genetic diversity is not well explored. The objective of this study was to generate high-quality genome assemblies for three Nguni ecotypes (Pedi, Venda, and Shangaan). Blood samples were collected from the three pure-breed Nguni ecotypes for library preparation and sequencing using PacBio Revio for HiFi reads and NovaSeq 6000 for Omni-C reads. The genomes were assembled using the Vertebrate Genome Project workflow implemented in Galaxy. The assembled genome sizes ranged from 3.12 Gb, 2.98 Gb and 2.99 Gb with a scaffold N50 of 107 Mb, 63 Mb and 61 Mb, contig N50 of 75 Mb, 63 Mb and 61 Mb, respectively. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness were 99.9 %, 96 % and 96 %, with k-mer completeness of 99.5 %, 99.6 % and 99.5 % for Pedi, Venda and Shangaan ecotypes respectively. Structural variant analysis uncovered breed specific diversity patterns, where Nguni Shangaan displayed the highest total variants counts of 1,418 with insertions representing the most predominant variant. The assemblies exhibit high contiguity and completeness, enabling accurate identification of structural variants and genome-wide restriction sites. Comparative analyses among the three ecotypes revealed genomic differences that may underlie ecotype-specific adaptations. These assemblies provide a valuable genomic resource for conservation, the development of breeding programs, and the study of adaptive traits in African cattle.

Keywords: 2026

How to Cite:

Mapholi, N., Tshilate, T., Smith, R., Molotsi, A., Hlongwane, N. & Nesengani, L., (2026) “High-quality genome assemblies of three Nguni cattle ecotypes using PacBio HiFi and Omni-C sequencing”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286292. doi: https://doi.org/10.31274/wcgalp.23909

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