Sequencing & Pangenomes

The First Telomere-to-Telomere Gap-Free Genome Assembly of Najdi Sheep: A Foundation for Desert-Adapted Livestock Genomics

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Abstract

Najdi sheep represent a culturally and economically significant breed indigenous to Saudi Arabia, exhibiting exceptional adaptability to harsh desert conditions. Despite their importance, comprehensive genomic resources for this breed remain severely limited. In this study, we generated the first telomere-to-telomere (T2T) gap-free genome assembly of Najdi sheep, providing an unprecedented genomic resource for understanding desert adaptation mechanisms and enabling precision breeding applications in arid environments. We used an integrated multi-platform sequencing strategy on a purebred male individual selected from a farm in the northern region of Saudi Arabia where the breed has been maintained without crossbreeding. Sequencing data included PacBio HiFi reads (40.31à—), Oxford Nanopore PromethION ultra-long reads (28.53à—), and Omni-C data (24.96à—). Primary assembly was performed using Hifiasm with default parameters, followed by gap-filling using ultra-long ONT reads. Telomeric regions were assembled by extracting HiFi reads containing ten or more copies of the canonical sheep telomere repeat sequence (AACCCT/AGGGTT), assembling these reads with unmapped and chromosome-end-mapping reads using Hifiasm, and integrating the resulting telomeric contigs with 1-Mb chromosomal end sequences using RagTag and validated by Omni-C contact maps. Our assembly achieved a genome size of 2.69 Gb with 99.993% base accuracy and complete resolution of all 26 autosomal chromosomes plus sex chromosomes X and Y. We successfully constructed all 56 telomeric regions across the 28 chromosomes. The assembly shows superior resolution in traditionally challenging genomic regions, particularly in centromeric and repetitive sequences, as demonstrated by increased abundance of Minimum Unique K-mers (MUKs) compared to existing sheep reference genomes. Gene annotation identified 97.2% of expected genes based on BUSCO analysis. Comparative genomic analysis with five genetically diverse sheep breeds (Awassi, Dorper, East Friesian, Merino, and Hu sheep) revealed breed-specific genetic signatures, with preliminary orthogroup analysis suggesting notable gene family expansions in Najdi sheep, particularly in genes potentially associated with desert adaptation and immune function. This complete genomic resource provides an essential foundation for genome-wide association studies targeting economically important traits including heat tolerance, disease resistance, and production efficiency. The comparative genomic analyses elucidate desert adaptation mechanisms, and the resource supports precision breeding programs to enhance livestock productivity in arid regions globally, representing a significant advancement in livestock genomics for climate-challenged regions worldwide.

Keywords: 2026

How to Cite:

BaAbdullah, M., Alarawi, M., Kulmanov, M., Abdulhakeem, M., Alghamdi, A., Alawwad, H., Alshehri, O., Almutairi, H., Almuhayya, A., Alhumaidy, A., Alajel, S. & Hoehndorf, R., (2026) “The First Telomere-to-Telomere Gap-Free Genome Assembly of Najdi Sheep: A Foundation for Desert-Adapted Livestock Genomics”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2295828. doi: https://doi.org/10.31274/wcgalp.24376

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