Background: Producers of cut flower chrysanthemum are obliged to manually remove lateral buds, a procedure which consumes one third of the total production cost. The formation of lateral buds in 'SEI NO ISSEI' is suppressed when the plants are exposed to high temperatures, but the molecular basis of this phenomenon is not well understood. Here, the transcriptome of buds formed by decapitated chrysanthemum plants grown under a high temperature regime was characterized with a view to revealing which genes known to be involved in a pathway determining shoot branching were induced/repressed by the treatment. Results: The transcriptomic data was acquired using RNA-Seq technology, based on the Illumina HiSeq™ 2000 platform. Four libraries were generated from pooled lateral buds of decapitated 'SEI NO ISSEI'. To predict the potential functions of unigenes in the 'SEI NO ISSEI' buds, after assembly, we performed seven functional database annotations. 132,396 unigenes were assembled, of which 79,116 unigenes were annotated in the seven functional databases. The percentage of unigenes annotated in the NR, NT, Swiss-Prot, KEGG, COG, Interpro, and GO databases were 54.59%, 42.96%, 39.05%, 41.84%, 20.72%, 37.25%, and 13.01%, respectively. Multiple differentially expressed transcription factors and auxin-related genes were identified in buds of decapitated 'SEI NO ISSEI' under 28°C/23°C or 38°C/33°C. Constitutively expressing CmERF110 in wild type Arabidopsis thaliana produced a bushy plant. A quantitative analysis of gene expression changes in the CmERF110 transgenic A. thaliana plants showed that the presence of the transgene altered the abundance of transcript produced by TIR1, ARF2, ARF16, IAA3 and IAA9 (encoding auxin signaling proteins) and PIN1, AUX1, LAX1, LAX2 and ABCB1 (auxin transport). Conclusions: This study reported a highly complete transcriptome from the buds of decapitated 'SEI NO ISSEI'. Differential abundant transcripts during high temperature treatments were identified and validated by qPCR, many of these differentially abundant transcripts as key players in bud outgrowth. These include known members of the AP2/ERF, MYB, WRKY, bHLH families and auxin-related genes. CmERF110 regulated shoot branching when its encoding gene was heterologously expressed in A. Thaliana. The regulation acted through the auxin-related genes. Background 4 The ability of the plant shoot to form branches has a major effect on the plant's architecture, a trait of major importance in the context of crop domestication and improvement [1, 2]. Axillary meristems are composed of a group of cells which have retained their meristematic potential [3]. Following their initiation, these structures develop into axillary buds, which either remain dormant or develop into a new branches, depending a number of both internal and/or external cues [4]. Three forms of bud dormancy have been recognized: paradormancy occurs when growth ceases because of physiological factors external to the bud; endodormacy when growth is regulated by internal physiologi...