The Emirati pangenome featuring a diploid chromosome-level reference

Reference genomes are essential for identifying and representing human genomic variation, yet single-genome sequences fail to capture population-specific diversity. We present the Emirati pangenome comprising a trio-based, diploid chromosome-level assembly from deep, multi-platform sequencing data and 57 additional high-quality HiFi sequencing-based chromosome-scale assemblies, 27 of which are trio-based. Haplotypes demonstrate high contiguity (median N50 of 151.9 Mb) and good base accuracy (median QV score of 59.31). Of all assembled chromosomes, 31.8% are telomere-to-telomere (T2T) scaffolds (chromosome-spanning sequences flanked by telomeric repeats at both ends), and 64.3% achieved chromosome-level continuity (single scaffolds spanning an entire chromosome but retaining one or more sequence gaps or lacking a telomeric signature at one or both ends). These assemblies form the foundation of the population-specific pangenome graph of the Emirati Reference Genome Project (ERGP), which captures genomic variation comparable to the globally diverse HPRC reference graph, while covering regionally enriched variation. Applying the ERGP pangenome to short‑read genotyping of an independent Emirati cohort revealed structural variant sites in linkage disequilibrium with phenotype‑associated GWAS variants, demonstrating the value of population-graph-based variant inference. The ERGP reference complements human pangenomes and provides a critical foundation for population-specific genomics and precision medicine in the United Arab Emirates. Here the authors present a chromosome-level Emirati pangenome, capturing population-specific genetic diversity and improving the detection of genomic variants. The resource will support more accurate genetic research and precision medicine in the United Arab Emirates.