Does Douglas-fir Celebrate the Solstice? Circadian and Circannual Cycles of Gene Expression Variation in Douglas-fir Needles

Perennial growth in plants is the product of interdependent cycles of daily and annual environmental stimuli that induce periods of physiological growth and dormancy. In conifers, leaves (“needles”) are a perennial organ that integrates seasonal signals from light, temperature and water availability. To understand the relationship between seasonal stimuli and seasonal responses in conifers, we examined transcriptome changes in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we generated 6.1x109 100 bp microreads from 19 trees and constructed a de novo pan- transcriptome reference that includes 162,326 transcripts. Using this reference, we mapped RNA-Seq reads from 166 samples that capture daily, seasonal, and annual variation. Our analysis identifies 15,487 diurnally-cycling transcripts, 4,912 of which show high amplitudes and include homologues to core clock genes from model plants. Analysis also reveals 24,688 annually-cycling transcripts, 11,963 of which show high amplitudes. The timing of maximum gene expression across diurnal and annual periods shows a bimodal response, with ~50% of transcripts reaching maximum expression +/- 2 hours from sunrise or sunset, and +/- 20 days from the shortest and longest photoperiod. The striking increase in transcription during short photoperiods is unusual because it coincides with dormancy; this may represent an exceptional case of transcriptional “anticipation” for the onset of spring growth. Our results implicate photoperiod as the dominant driver of annual transcription patterns and may be general for temperate zone conifers, making them useful for predicting rhythmic transcription in newly-emerging conifer models.