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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Improvement Research » Research » Publications at this Location » Publication #437136
Research Project: Improvement of Disease and Pest Resistance in Barley, Durum, Oat, and Wheat Using Genetics and Genomics

Location: Cereal Crops Improvement Research

Title: A subgenome-resolved and chromosome-scale reference genome assembly of allotetraploid wheat wild relative Aegilops peregrina

Author
item SINGH, JATINDER - North Dakota State University
item GUDI, SANTOSH - North Dakota State University
item MAUGHAN, JEFF - Brigham Young University
item UPINDER, GILL - North Dakota State University
item Gupta, Rajeev

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 8/28/2026
Publication Date: 8/30/2026
Citation: Singh, J., Gudi, S., Maughan, J., Upinder, G., Gupta, R. 2026. A subgenome-resolved and chromosome-scale reference genome assembly of allotetraploid wheat wild relative Aegilops peregrina. bioRxiv. https://doi.org/10.64898/2026.08.28.747929.
DOI: https://doi.org/10.64898/2026.08.28.747929

Interpretive Summary: Wheat is one of major cereals and provides approximately one-fifth of the calories consumed globally. But its genetic diversity is constrained by the limited number of hybridization events involved in the origin of hexaploid wheat. Wheat wild relatives in the genus Aegilops represent an important reservoir of genetic diversity for various stress resilience and agronomic traits for improvement of wheat. Here, we present a subgenome-resolved, chromosome-scale reference genome assembly of Aegilops peregrina. This chromosome-scale reference genome establishes a genomic resource that will facilitate sequence-level characterization and deployment of disease and pest resistance in wheat improvement.

Technical Abstract: Aegilops peregrina is a wild allotetraploid wheat wild relative and an important source of genetic diversity for stress tolerance and agronomic traits. Here, we report a subgenome-resolved, chromosome-scale reference genome assembly of a drought tolerant and stem rust resistant Ae. peregrina accession PI 604178 generated using PacBio HiFi and Hi-C sequencing. The 10.13 Gb assembly contains 98.81% of sequence anchored to 14 pseudomolecules representing the seven S' and seven U' chromosomes, with contig and scaffold N50 values of 25.84 and 746.48 Mb, respectively. The assembly achieved a consensus quality value of 74.61, 97.83% k-mers completeness, and 99.9% BUSCO completeness. LTR Assembly Index values of 20.43 and 18.79 for the S and U subgenomes, respectively, further supported high continuity across repeat-rich regions. Repetitive elements comprise 85.93% of chromosome-anchored assembly. We annotated 59,910 high-confidence protein-coding genes, with comparable gene representation across the two subgenomes. This reference genome provides a high-quality genomic framework for comparative analyses, characterization of important loci regulating agronomic and resilience related traits, and sequence-guided exploitation of Ae. peregrina allelic diversity for wheat improvement.