Multi-omics analyses reveal transposon-associated genomic evolution and regulatory rewiring in barley 

Background: Transposable elements (TEs) are major components of plant genomes and possess the capacity to transpose across genomes. Nevertheless, their associations with DNA methylation landscapes and three-dimensional (3D) genome organization in barley ( Hordeum vulgare ) remain poorly understood. Results: Here, we performed integrated comparative genomic, methylomic, population genomic and Hi-C analyses to investigate the associations between TEs and barley genome evolution and domestication. We found that continuous proliferation of long terminal repeat (LTR) retrotransposons is strongly associated with the barley genome expansion and with distinct genome-wide DNA methylation landscapes across plant species. Population genomic analyses identified candidate domestication-associated genes enriched in sucrose metabolism pathways and revealed an exceptionally slow decay of linkage disequilibrium in barley. Comparative Hi-C and genomic analyses further uncovered extensive differences in A/B chromatin compartments and divergence of topologically associating domains (TADs) between wild and domesticated barley, and indicated that regulatory rewiring, rather than widespread gene gain or loss, represents a prominent feature during barley domestication. Notably, the enrichment of DNA transposons and Copia retrotransposons at TAD boundaries suggested a potential role for TEs in higher-order chromatin organization. Conclusions: Together, our study provides valuable genomic resources for future functional investigations in barley and underscores the potential value of incorporating 3D genome features into molecular breeding strategies.