A Near Telomere-to-Telomere Reference Genome for Drakensberger Cattle Achieved Through Trio-Binned Long-Read Sequencing

Abstract

Drakensberger cattle is indigenous to South Africa and represent a unique genetic resource which is known for its quality beef production and adapted to the harsh climatic conditions. Despite its significance within the beef industry, no high-quality chromosomal level genome has been reported for this breed, limiting genomic selection and conservation efforts. Although there is a bovine genome reference, we need a breed specific reference to identify breed-unique alleles and structural variants that might not be explained by a distant reference. To address this, we generated a haplotype resolved assembly for Drakensberger cattle using a trio-binning where we employed PacBio HiFi reads for sire and dam, a combination of PacBio HiFi reads, Oxford Nanopore Technologies reads and Omni-C reads for the offspring. The assembled diploid genome size is 2.89 Gb with a scaffold N50 of 111 Mb and contig N50 of 61 Mb. The consensus accuracy was exceptionally high (QV = 70.23) and a genome completeness of 97.5 %, as analysed by the Benchmarking Universal Single-Copy Orthologs (BUSCO). The k-mer profiling suggested one of the strong haplotype separation for livestock with the paternity assembly containing 97.1% and maternity with 99.0%, combined diploid genome recovered 99.46% of all the solid read k-mers. We identified 14 telomeric ends across 13 scaffolds. The final genome encompassed a total of 22,854 protein-coding genes. This is the first high-quality, haplotype resolved genome assembly of the Drakensberger breed. This assembly high accuracy, contiguity and completeness place the genome among the highest-quality cattle genomes produced to date. This genomic resource is essential in designing programs to studies for breed evolution, adaptation, genomic selection and for conservation of the South African indigenous resources.