Functional landscape of repetitive elements in the Nguni sheep genome
- Thendo Tshilate (University of South Africa)
- Lucky Nesengani (University of South Africa)
- Rae Smith (University of South Africa)
- Sinebongo Mdyogolo (University of South Africa)
- Annelin Molotsi (University of South Africa)
- Sibusiso Hadebe (University of South Africa)
- Nompilo Hlongwane (University of South Africa)
- Tracy Masebe (University of South Africa)
- Ntanganedzeni Mapholi (University of South Africa)
Abstract
Nguni sheep are an indigenous South African breed valued for their adaptation to local smallholder farming systems. While a genome assembly is available, the genomic drivers of their evolution and adaptive traits remain largely unexplored. Transposable elements (TEs) are powerful agents of genome evolution. This study investigates their relationship with gene content in the Nguni sheep genome to understand their potential role in the breed's distinctive biology. Repetitive sequences were identified using RepeatMasker against the Dfam database, and their overlap with protein-coding genes was analyzed with BEDTools. The most repeat-dense genes were characterized and their protein sequences functionally annotated using EggNOG-mapper. Results revealed extensive TE-gene overlap, predominantly involving Simple Repeats, LINEs, and SINEs. Functional annotation of these genes showed significant enrichment for biological processes related to immune response (DOCK2), neuronal development (CADPS, TENM2), and kinase activity (ULK4), which are linked to pathways such as calcium signalling and leukocyte trans-endothelial migration. While these initial findings highlight a notable prevalence of retrotransposons, particularly SINEs and LINEs, within genic regions, their specific regulatory impact requires further validation. Future comparative analysis with genomes of major commercial breeds will be essential to determine whether these TE-gene associations are unique to Nguni sheep or represent conserved features, thereby clarifying their contribution to the breed's renowned adaptation plasticity. This study provides a foundational characterization of repetitive elements in the Nguni genome, linking them to functional genes that may underpin adaptive traits like disease resistance and environmental resilience.
Keywords: 2026
How to Cite:
Tshilate, T., Nesengani, L., Smith, R., Mdyogolo, S., Molotsi, A., Hadebe, S., Hlongwane, N., Masebe, T. & Mapholi, N., (2026) “Functional landscape of repetitive elements in the Nguni sheep genome”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286673. doi: https://doi.org/10.31274/wcgalp.24090
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