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Maintaining the viability of the apical shoot is critical for continued vertical growth in plants. Terminal shoot of tree species  Paulownia  cannot regrow in subsequent years. The short day (SD) treatment leads to apical growth cessation and dormancy. To understand the molecular basis of this, we further conducted global RNA-Seq based transcriptomic analysis in apical shoots to check regulation of gene expression. We obtained ~219 million paired-end 125-bp Illumina reads from five time-courses and  de novo  assembled them to yield 49,054 unigenes. Compared with the untreated control, we identified 1540 differentially expressed genes (DEGs) which were found to involve in 116 metabolic pathways. Expression of 87% of DEGs exhibited switch-on or switch-off pattern, indicating key roles in growth cessation. Most DEGs were enriched in the biological process of gene ontology categories and at later treatment stages. The pathways of auxin and circadian network were most affected and the expression of associated DEGs was characterised. During SD induction, auxin genes  IAA ,  ARF  and  SAURs  were down-regulated and circadian genes including  PIF3  and  PRR5  were up-regulated.  PEPC  in photosynthesis was constitutively upregulated, suggesting a still high CO 2  concentrating activity; however, the converting CO 2  to G3P in the Calvin cycle is low, supported by reduced expression of  GAPDH  encoding the catalysing enzyme for this step. This indicates a de-coupling point in the carbon fixation. The results help elucidate the molecular mechanisms for SD inducing dormancy and cessation in apical shoots.

Time-coursed transcriptome analysis identifies key expressional regulation in growth cessation and dormancy induced by short days in Paulownia