PacBio HiFi
The sample collection procedure including processing and handling of the animals used in this study was approved by the University of South Africa ethics committee (reference number: AREC-100818-024) and the Department of Agriculture Land Reform and Rural Development (DALRRD) under section 20 of the Animal Diseases Act 1984 (Act 35 of 84) (ref no 12/11/1/1/23 (6508 AC). Furthermore, the ethics procedure was guided by the AfricaBP policy on ethics which emphasises ethical, legal, and social issues throughout the research activities. Sample collection and sequencing: In this study, a pure breed of ewe Nguni sheep was selected from Mara research station (Figure 1B) herd for sampling in Limpopo province of South Africa (23 05'S, 29 25'E). Blood was collected from the jugular vein in EDTA tubes by the veterinarian and placed on dry ice, immediately transported to Inqaba Biotech laboratories, and stored at -80C freezer until further processing. High molecular weight genomic DNA was extracted from 200 ul blood using Nanobind protocol for whole blood high molecular weight (HMW) DNA extraction to construct a sequencing library. The protocol was optimised for extraction from 200 ul of whole blood. Library sequencing on the PacBio Sequel IIe platform was done using SMRTbell prep kit 3.030 following the manufacturers instructions. Dovetail Omni-C library prep was performed from the same sample used for HiFi sequencing following the manufacturers instructions. The resulting library was sequenced on NovaSeq 6000 instrument (Illumina). The total HiFi output data was 99 Gb at a coverage of 30 while the output for Omni-C was 300 million read pairs.