Conservation & local programs

Whole genome sequencing of the Southern White Rhino (Ceratotherium simum) genome in efforts to its conservation in South Africa.

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Abstract

Southern White Rhinos (SWR) are known for their distinctive two horns. It was once on the brink of extinction and was listed on the IUCN Red List of Threatened Species in 2020 as Near Threatened. This has led to increased conservation efforts, and in-situ breeding programs have been perpetuated in Southern Africa. Currently, both a draft genome and chromosomal level genome are available for the Southern White Rhino, which was sequenced using Illumina short reads and PacBio HiFi reads, respectively. However, there are no studies available on the structural variants for SWR in South Africa. Therefore, this study aimed to assemble the Southern White Rhino using HiFi long reads and to elucidate the genetic regions linked to specific phenotypic traits. Blood samples were obtained from 1 female SWR, and HMW DNA was extracted for SMRTbell library preparation for PacBio Revio HiFi sequencing. The total data yielded was 13.3 Gb with a genome coverage of 5.7X. The genome size was 2.3 Gb and the scaffold N50 67 Kb with a scaffold N50 of 9,737. The number of scaffolds was 45,369, with an average scaffold length of 50,792.93 Kb and a GC content of 39,82%. These results were obtained using the HiFiasm assembler. The assembly was further subjected to purging of duplicates using the Purgedups v1.2 .pipeline. After purging, the number of scaffolds decreased to 39,464, and the scaffold N50 is 70 Kb, and the scaffold L50 is 8,690. Due to the low coverage obtained from the HiFi sequencing, we aligned the raw reads to a chromosomal-level SWR assembly using minimap2. This was followed by sorting and the removal of duplicates using SAMtools, whereafter SNP variants were called using snpEff v5.3. Structural variants were detected using Sniffles 2. The number of variants identified was 1,154,334, including 1,279 high-impact SNP effects. The Transitions/Transversions ratio was 1.79. Enrich R gene ontology analysis yielded significant biological pathways, including the Regulation of Calcium Ion Transmembrane Transport via High Voltage-Gated Calcium Channel, Protein Localization to Cell Junction, Regulation of Microtubule Depolymerization, GTP Metabolic Process, and Taurine Metabolic Process. Mutations in the genes linked to the biological pathways mentioned above could be associated with diseases and reproduction traits in the SWR. Therefore, further studies including phenotypic data on specific diseases and reproduction are needed to validate these findings.

Keywords: 2026

How to Cite:

Molotsi, A., Tshilate, T., Nesengani, L., Mdyogolo, S., Smith, R., Hlongwane, N., Hadebe, S., Masebe, T., Mafokwane, T. & Mapholi, N., (2026) “Whole genome sequencing of the Southern White Rhino (Ceratotherium simum) genome in efforts to its conservation in South Africa.”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286380. doi: https://doi.org/10.31274/wcgalp.23971

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