A high-quality chromosome level genome assembly of the South African indigenous Nguni goat (Capra hircus)

Abstract

Nguni goat is an indigenous goat breed of South Africa characterised by small body frame, variable coat colours and exceptional tolerance to harsh environmental conditions. This breed is utilised for meat and milk production thus sustaining the livelihood of communal farmers and is important for cultural purposes. We assembled a high-quality genome using HiFi and Omni-C reads. For HiFi and Omni-C, we used PacBio sequel IIe and the Illumina NovaSeq 6000, respectively. The total HiFi generated was 106 Gb and Omni-C generated 300 million reads. The assembly length was 2.85 Gb, comprising of 114 scaffolds and 127 contigs; with N50/L50 of 97.7 Mb/12 and 81.34 Mb/12, respectively. BUSCO showed 96% completeness with 3% missing genes making it the most complete genome. The genome contained 42.86% repetitive elements, with LINEs being the most abundant, representing 28.82% and accounting for 67% of total repeats. The annotation predicted 22,507 genes with an average length of 33,847.2 bp. The genome assembly of the Nguni goat will advance genomic research and enhance breeding programs to improve both production and conservation.