A Study of Aegilops Genomes: Towards Understanding Their Evolution and Potential for Wheat Improvement

Abstract

Crop improvement has historically relied on the continuous enhancement of yield, adaptability, and resilience, yet polyploidization, domestication and modern breeding have narrowed the genetic diversity of cultivated wheat. Wild relatives, particularly species within the genus Aegilops, represent a critical reservoir of untapped genetic variation with the potential to address emerging agricultural challenges. Despite their evolutionary and agronomic importance, genomic resources for many Aegilops species have remained limited, restricting comprehensive investigations of their genome evolution and utilization in wheat improvement.

In this study, high-quality genome assemblies and gene annotations were generated for 18 diploid, tetraploid, and hexaploid Aegilops species, which, together with previously published genomes, complete a reference set for all 25 species within the genus. Assembly sizes ranged from 5.24 Gb in diploids to 12.65 Gb in polyploids, with high contiguity enabling detailed analyses of complex and repeat-rich genomic regions. Gene annotation provided a comprehensive overview of protein-coding gene content across all assembled Aegilops genomes. The annotated gene sets offer a consistent resource for comparative genomic analyses and functional exploration across the genus.

Phylogenetic reconstruction based on near single-copy orthologs across Triticum and Aegilops genomes provided a well-resolved evolutionary framework and confirmed relationships between polyploid genomes and their diploid progenitors. Divergence time estimates further contextualized species evolution within the genus. Comparative analyses of structural variation revealed extensive genome restructuring following polyploidization, including insertions, deletions, duplications, and rearrangements, while maintaining overall syntenic conservation. These patterns highlight the dynamic nature of polyploid genomes and their divergence from ancestral states.

Genome-wide characterization of transposable elements revealed that Aegilops genomes are dominated by long terminal repeat (LTR) retrotransposons, with evidence of both conserved and subgenome-specific patterns of expansion and contraction. Temporal analyses of LTR insertions indicated variation in insertion activity over time, reflecting differences in transposable element dynamics among species and subgenomes.

Together, these results provide a comprehensive and integrative view of genome evolution in Aegilops, linking genome structure, transposable element dynamics, and evolutionary history across ploidy levels. The genomic resources and insights generated in this study not only advance our understanding of polyploid genome evolution but also provide a valuable foundation for harnessing Aegilops diversity to improve the resilience, adaptability, and productivity of cultivated wheat.