Comparative phylogenomics reveals multilevel genomic differentiation between annual and perennial Hordeum species

Annual plants complete their life cycle with a single reproductive episode, whereas perennials must balance reproduction with the maintenance of tissues that sustain future growth. Despite the fundamental importance of this distinction, the genomic differences associated with these contrasting life histories remain poorly understood. Here, we utilize independent occurrences of annuality in the grass genus Hordeum to identify recurrent differences between annual and perennial species. Combining transcriptomes from 82 accessions with recently published reference genomes, we compared protein-coding sequence evolution, gene copy number, gene expression and co-expression while accounting for evolutionary non-independence. We found widespread genomic differentiation, with several consistent patterns. Genes involved in cell division and genome maintenance showed evidence of stronger evolutionary constraint in perennials, while gene families associated with developmental regulation and senescence were more frequently retained in higher copy numbers in perennials. Differences in gene expression and coordination were particularly pronounced during reproduction, when perennials showed higher expression of genes involved in cell division, cytoskeletal organisation, cell-wall formation and resource transport, together with extensive reorganisation of gene co-expression relationships. Across these complementary analyses, processes involved in cellular proliferation, developmental regulation and tissue maintenance repeatedly distinguished the two life histories. Our findings suggest that annual-perennial differentiation extends beyond individual flowering regulators to broader genomic differences associated with a more complex coordination of processes balancing growth and senescence in perennials. By identifying these recurrent patterns across evolutionary lineages, this study provides a comparative framework for understanding the genomic differentiation underlying contrasting plant life histories.