Kudo, S. N. | bioRxiv Science

bioRxiv2025

Molecular evolution of terpene synthase underlying the diversification of isoprene emission in Fagaceae

Plants emit a wide range of volatile organic compounds, among which isoprene is the most abundant and atmospherically influential. Although oak species are major contributors to isoprene emission, there is considerable variation in isoprene emission capacity within the Fagaceae family. To unravel the evolutionary origins of isoprene emission, we investigated the molecular evolution of terpene synthase (TPS) genes across eight species within the Fagaceae. We identified a Fagaceae-specific TPS-b subclade in which potential isoprene synthase (IspS) activity evolved independently in two gene lineages within subgenus Quercus. Ancestral sequence reconstruction revealed that the acquisition of a diagnostic amino acid residue for IspS function arose convergently in these lineages and was subject to positive selection, suggesting adaptive evolution. Ancestral-enzyme assays targeting the gene lineage with high gene expression revealed that the early protein primarily produced monoterpenes from geranyl diphosphate (GPP), whereas their descendants shifted substrate preference to dimethylallyl diphosphate (DMAPP), evolving into dedicated isoprene synthases. Our results indicate that IspS activity was not ancestral in Fagaceae, but evolved approximately 56 million years ago within the subgenus Quercus, and has been retained ever since. These findings emphasize the roles of enzyme structural innovation and regulatory shifts in the diversification of volatile terpenoid biosynthesis.

evolutionary biology↗

bioRxiv2025

The evolution of gene expression in seasonal environments

The biological activities of organisms are closely linked to seasonality. Phenology, the temporal orchestration of biological activities, is governed by gene expression, yet the evolutionary dynamics underlying seasonal gene expression remain unclear. To investigate these dynamics, we compared genome-wide expression dynamics (molecular phenology) in four dominant evergreen Fagaceae species in Asia (Quercus glauca, Q. acuta, Lithocarpus edulis, and L. glaber), using leaf and bud tissues over two seasonal cycles. We assembled high-quality reference genomes, identifying 11749 single-copy orthologous genes. Seasonal transcriptomic profiling of these orthologous genes revealed highly conserved gene expression across species in winter when temperatures fall below [~]10{degrees}C. Rhythmic gene expression with significant periodic oscillations was more prevalent in buds (51.9%) than in leaves (40.6%), with most rhythmic genes (78.4-92.0%) exhibiting annual periodicity, while a smaller fraction (1.2-11.9%) followed half-annual cycles. The seasonal peaks of rhythmic genes were highly synchronized across species in winter but diverged during the growing season, reflecting species-specific timing of leaf flushing and flowering. These findings suggest that the four species share a common molecular calendar in winter, which constrains the evolution of gene expression under seasonal environments. Impact StatementA comparative analysis of genome-wide seasonal gene expression dynamics across four forest tree species revealed that a shared "molecular calendar" emerges in winter, constraining gene expression evolution and potentially limiting temporal niche partitioning and species divergence in seasonal environments.

evolutionary biology↗