Circadian Timekeeping in the Tropics: Rhythmic Transcriptome and Diurnal Regulatory Networks in Rubroshorea leprosula

Circadian rhythms allow plants to regulate internal processes to align with daily rhythms in the environment. Comparing circadian clocks across environments is essential because latitude-dependent variation in light and temperature imposes distinct selection pressures that shape the evolution and function of circadian timing systems. However, circadian clock studies have largely focused on temperate and subtropical species, leaving transcriptional circadian networks in tropical plants poorly understood. We report the comprehensive circadian transcriptome of Rubroshorea leprosula, a dominant species in tropical rainforests in Southeast Asia. One sapling was sampled every 4 hours over 48-hour period under constant darkness and used for transcriptomic analyses. Only 283 of 20 748 expressed genes (~1.3%) exhibited significant circadian oscillations, with periods strongly concentrated between 23 and 25 hours. Hierarchical clustering revealed 4 temporal clusters with alternate phases of expression and functional specialization. Comparative analysis identified clear orthologs for all major Arabidopsis circadian clock components, with conserved synteny to Parashorea chinensis, a close relative of R leprosula. Time-lagged cross-correlation network reconstruction identified a characteristic circadian topological similarity with Arabidopsis, including coupled morning and evening feedback loops and paralog expansion that maintained overall structure. Peak expression timing of these core clock genes in the tropical tree was largely consistent with that observed in Arabidopsis thaliana. In contrast, Rubroshorea orthologs showed reduced amplitudes and lower coefficients of variation under this single constant darkness, single-individual condition; because dark-induced damping is common across plants, this pattern is consistent with, but does not establish, reduced circadian robustness in R leprosula linked to tropical adaptation. This study lays the molecular foundation for circadian regulation in dipterocarps and offers a system for integrating rhythmic gene expression to ecological function and forest productivity in tropical communities.