Emirati pangenome maps regional genome variation at chromosome scale

A population-specific Emirati pangenome has produced a diploid chromosome-level reference assembly and integrated additional chromosome-scale assemblies to represent human genomic variation found in the United Arab Emirates. The project generated one trio-based assembly from deep, multi-platform sequencing data and 57 additional high-quality HiFi sequencing-based chromosome-scale assemblies, 27 of which were also trio-based. Its pangenome graph captured variation comparable to that represented in the globally diverse Human Pangenome Reference Consortium graph while including regionally enriched variation.

The work addresses a central limitation of single-genome references: one assembled sequence does not represent the full range of genetic variation across a population. For the Emirati Reference Genome Project, researchers assembled multiple human genomes and combined their haplotypes in a population-specific pangenome graph. The central assembly was diploid and trio-based, while the broader collection included HiFi sequencing-based chromosome-scale assemblies. This design links individual chromosome assemblies to a graph intended to preserve both shared sequence and population-level variation.

Assembly quality was assessed through contiguity, base accuracy and the completeness of chromosome-scale scaffolds. Across the assembled haplotypes, the median contiguity N50 was 151.9 megabases and the median base-accuracy QV score was 59.31. Of all assembled chromosomes, 31.8% were telomere-to-telomere scaffolds, defined in the study as chromosome-spanning sequences flanked by telomeric repeats at both ends. Another 64.3% achieved chromosome-level continuity, comprising a single scaffold that spanned an entire chromosome but retained one or more sequence gaps or lacked a telomeric signature at one or both ends. Thus, the results show substantial chromosome-scale representation, while not every assembled chromosome met the stricter telomere-to-telomere criterion.

The researchers next applied the ERGP pangenome to short-read genotyping in an independent cohort of Emirati participants. This analysis identified structural-variant sites in linkage disequilibrium with phenotype-associated variants from genome-wide association studies. The observation shows that the population graph supported structural-variant inference in this cohort and recovered sites associated with previously reported phenotype-associated loci through statistical linkage. It does not establish that the structural variants cause the associated phenotypes, nor does it demonstrate clinical effectiveness.

The Emirati pangenome complements existing human pangenome resources by incorporating a population-specific collection of chromosome-scale assemblies and a graph that includes regionally enriched variation. The reported results provide a reference foundation for population-specific genomics in the United Arab Emirates. The authors identify potential relevance to population genomics and precision medicine, but the evidence presented here is limited to assembly quality, graph coverage and structural-variant inference in one independent Emirati cohort; no direct clinical benefit was tested or demonstrated.

Subject of Research: Construction and evaluation of a population-specific Emirati human pangenome and diploid chromosome-level reference

Article Title: The Emirati pangenome featuring a diploid chromosome-level reference

Article References: Olbrich, M., Mousa, M., Wohlers, I., Al-Aamri, A., Alnaqbi, H., Alsuwaidi, A. H., Manoharan, H. V., Marzouka, N. A.-D., Bartels, L., Ramachandran, S. E., Thomas, A. A., Gasso, M. P., Almehairbi, M., Alameri, M., Tay, G., Hamoudi, R., Ibrahim, S., Al Ghaithi, N., & Alsafar, H. (2026). The Emirati pangenome featuring a diploid chromosome-level reference. Nature Communications. https://doi.org/10.1038/s41467-026-78776-3

Image Credits: AI Generated

DOI: 10.1038/s41467-026-78776-3

Keywords: Emirati pangenome, human genomics, reference genome, diploid assembly, pangenome graph, structural variation, chromosome sequencing, HiFi sequencing, United Arab Emirates, Emirati, pangenome, featuring