[SS11] Interdisciplinary approaches to diverse biological rhythms

[SS11-03] Seasonal Rhythms in Genome-wide Gene Expression in Forest Trees

*Shuichi Kudo¹, Yuka Ikezaki¹, Junko Kusumi¹, Hideki Hirakawa¹, Sachiko Isobe², Akiko Satake¹ (1. Kyushu Univ. (Japan), 2. Tokyo Univ. (Japan))

Keywords:

phenology,gene expression evolution,seasonal constraints

The life histories of organisms are closely linked to seasonality. Phenology, the temporal coordination of biological activities, is governed by gene expression dynamics, yet the evolutionary mechanisms shaping seasonal gene expression remain unclear. Here, we compare genome-wide expression dynamics under natural seasonal conditions (molecular phenology) in four dominant evergreen Fagaceae species (Quercus glauca, Q. acuta, Lithocarpus edulis, and L. glaber), using leaf and bud tissues over two seasonal cycles. We first assembled high-quality reference genomes for Q. glauca and L. edulis, identifying 11749 single-copy orthologous genes. Seasonal transcriptomic profiling revealed highly conserved gene expression across species in winter, particularly in buds, when temperatures fall below ~10°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, aligning with key phenological events such as leaf flushing and flowering. Genes with conserved seasonal peaks exhibited slower protein coding-sequence evolutionary rates, suggesting weak selective pressures maintaining seasonal gene expression. However, the evolutionary rates were similarly slow regardless of whether genes were expressed in winter or the growing season. These findings suggest that winter gene expression is more conserved than that in the growing season, imposing a seasonal constraint on gene expression evolution. This constraint may limit temporal niche partitioning and slow species divergence rates in seasonal environments.