Transcription through the eye of a needle: Daily and annual cyclic gene expression variation in Douglas-fir needles

Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, Jill L. Wegrzyn, David B. Neale, J. Bradley St. Clair, Dee R. Denver

Research output: Contribution to journalArticlepeer-review

28 Scopus citations


Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1×109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/- 2h from sunrise and sunset, and +/- 20days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. Conclusions: Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.

Original languageEnglish (US)
Article number558
JournalBMC Genomics
Issue number1
StatePublished - Jul 24 2017

Bibliographical note

Funding Information:
This project was supported by the US Department of Agriculture National Institute of Food and Agriculture (Plant Genome, Genetics and Breeding Program #2010–65,300-20,166) and the US Forest Service Pacific Northwest Research Station. These funding agencies provided peer review for the original proposal, but played no role in the design of the study, sample collection, analysis or interpretation of the data.

Publisher Copyright:
© 2017 The Author(s).


  • Circannual
  • Diurnal
  • Dormancy
  • Douglas-fir
  • Pseudotsuga menziesii
  • RNA-Seq
  • Transcriptome


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