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

BMC Genomics

Research Article

Jill L. Wegrzyn¹  Dee R. Denver²  Sanjuro Jogdeo²  David B. Neale³  Richard Cronn⁴  J. Bradley St. Clair⁴  Peter C. Dolan⁵ 

[1] Department of Ecology and Evolutionary Biology, University of Connecticut, 06269, Storrs, CT, USA;Department of Integrative Biology, Oregon State University, 97331, Corvallis, OR, USA;Department of Plant Sciences, University of California – Davis, 95616, Davis, CA, USA;Pacific Northwest Research Station, USDA Forest Service, 97331, Corvallis, OR, USA;University of Minnesota – Morris, 56267, Morris, MN, USA;

关键词: Circannual;    Diurnal;    Dormancy;    Douglas-fir;    Pseudotsuga menziesii;    RNA-Seq;    Transcriptome;   

DOI  :  10.1186/s12864-017-3916-y

 received in 2016-11-17, accepted in 2017-06-30,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundPerennial 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.ResultsWe 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 +/− 2 h from sunrise and sunset, and +/− 20 days 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© The Author(s). 2017

【 图 表 】

12864_2017_3916_Article_IEq1.gif