Fundamental biological processes, such as growth, mortality, and reproduction, rarely remain constant over time; instead, they exhibit pronounced variation in response to seasonal environmental changes (Fretwell, 1972). This temporal organization of a series of biological activities, known as phenology, plays a critical role in the evolution of life histories in response to seasonal fluctuating environments (Forrest and Miller-Rushing, 2010; Morellato et al., 2013; Piao et al., 2019; Schwartz, 2013). Phenology is regulated by the coordinated expression of genes that enable organisms to exhibit essential functions at the appropriate times (Kudoh, 2016; Satake et al., 2024a; Satake et al., 2022). However, gene expression dynamics underpinning seasonal responses in organisms remain not fully understood.
To explore the evolution of gene expression, transcriptome analyses are widely employed to compare transcript profiles across organs, sexes, species, and developmental stages within a given environment. Such studies have been conducted in mammals (Brawand et al., 2011; Cardoso-Moreira et al., 2019; Naqvi et al., 2019), Drosophila (Lemos et al., 2005; Nuzhdin et al., 2004), and Tanzanian cichlids (El Taher et al., 2021), providing key insights into the evolutionary dynamics of gene expression and its central role in shaping phenotypic diversity. These studies have revealed that gene expression profiles tend to be more conserved across species within the same tissue, whereas the evolutionary rate of gene expression varies among organs. In mammals, for instance, nervous tissue exhibits a slower rate of gene expression change compared to the testis (Brawand et al., 2011; Cardoso-Moreira et al., 2019; Naqvi et al., 2019), suggesting the presence of tissue-specific functional constraints that influence the evolution of gene expression.
In addition to tissue-dependent constraints, seasonal environmental changes may play a crucial role in shaping the evolution of gene expression, particularly by influencing the temporal coordination of gene expression under natural conditions. Gene expression responses to certain seasons may be more resistant to change, whereas in other seasons, divergence in gene expression timing across species may occur, contributing to temporal niche differentiation. Despite its potential importance, the influence of seasonal environmental fluctuations on the gene expression evolution remains poorly understood, largely because most transcriptomic analyses have been conducted under tightly controlled laboratory conditions.
To investigate the evolution of gene expression in seasonal environments, we performed a molecular phenology analysis and phenological observation of leaf flushing and flowering in Fagaceae tree species, which are widely distributed across the Northern Hemisphere, with its center of diversity in subtropical Southeast Asia (Hipp et al., 2020; Kremer et al., 2012; Manos et al., 2001; Zhou et al., 2022). Molecular phenology refers to transcriptome analysis conducted under natural fluctuating conditions (Komoto et al., 2024; Kudoh, 2016; Nagano et al., 2019; Satake et al., 2023) and provides a valuable framework for studying gene–environment interactions and their role in orchestrating the temporal biological functions essential for adaptation to environmental fluctuations (Satake et al., 2022). In this study, we selected four evergreen Fagaceae species—two Quercus species (Q. glauca and Q. acuta) and two Lithocarpus species (L. edulis and L. glaber)—that co-occur in the same locality in Japan. Q. glauca, L. edulis, and L. glaber inhabit nearly identical environment, while Q. acuta is restricted to the high-altitude regions with slightly colder environment compared to the other three species. Leaf flushing and flowering phenology vary across species, with Q. glauca and Q. acuta flowering in early spring, almost simultaneously with leaf flushing, L. edulis flowering in late spring, and L. glaber flowering in autumn, approximately one to two months after leaf flushing. This setting enabled us to compare seasonal gene expression profiles across species with diverse phenology, both within and between genera, under nearly identical environmental fluctuations. By assessing and comparing seasonal transcriptomic dynamics across Fagaceae species, our study provides new insights into the evolution of gene expression and adaptation to seasonal natural environments.