Transcriptome dynamics of daily, seasonal and annual cycles in the needles of Douglas-fir (Pseudotsuga menziesii Mirb.)

Rhythms of light, temperature, and precipitation provide signals that regulate rhythmic gene expression and growth in trees. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal, seasonal, and circannual needle mRNA accumulation in Douglas-fir, Pseudotsuga menziesii. Using mRNA sequencing, we sampled 101 bp reads from 19 trees and constructed a combined 'pan-transcriptome' reference that includes 199,471 transcripts (PRJNA356432). Using this reference, we mapped RNA-seq reads from samples that capture diurnal variation between two families of trees (12 time points; PRJNA263611), seasonal variation between three families of trees (PRJNA188506), and annual variation between two families of trees (16 time points; PRJNA243096). This study shows that thousands of genes reach peak annual activity during the winter and summer solstices, and that photoperiod and light quality is a dominant driver of daily and annual transcription in Douglas-fir.