*2.4. Plant Materials, Transcriptome Sequencing, RNA Isolation and Reverse Transcription, Heat Map and qRT-PCR*

Healthy passion fruit seedlings about two months old (30 cm in height) in the soil were chosen. The seedlings were planted in incubators and treated with cold, high temperature, high salt, and drought stresses. The control was placed in incubators (28 ◦C, 70% relative humidity, 12 h light/12 h dark cycle, 200 μmol m−<sup>2</sup> s−<sup>1</sup> light intensity). In addition, after fruit ripening, the pericarp turns purplish red. The three stages (T1, T2, and T3) are the time of 7d before ripening, ripening, and 7d after ripening, respectively [45]. The experimental material consisted of three biological replicated samples. The plant materials were used for transcriptome sequencing. The expression data of *PebHLHs* at four stress and three fruit ripening stages are shown in Tables S2 and S4. TBtools software was used for transcriptional analysis of *PebHLHs*, whose Z-score normalized FPKM values were used to produce heat maps [47]. The plant RNA isolation kit was used in *Arabidopsis* transformed with pCAMBIA1304-*PebHLH56*. The Biomic Biotechnology company (Beijing, China) was entrusted with sequencing services. The Primer sequences of *PebHLHs* were designed using the Primer5 software. The expression of *PebHLHs* was detected by qRT-PCR analysis. Relative expression levels were calculated using the 2−ΔΔCt method and normalized to the *PebHLHs*.

#### *2.5. Cloning the Promoter of PebHLH56 and Vector Construction*

A 2000 bp DNA sequence before the start codon of the PebHLH56 was amplified by PCR and cloned into the pMD19-T vector. The promoter of PebHLH56 was assessed by DNA-MAN.

Expression vectors were constructed to examine whether *PebHLH56* responds to cold stress. The *PebHLH56* promoter PCR fragment was cloned into the pCAMBIA1304 vector digested with NcoI/HinIII, which was called pCAMBIA1304-*PebHLH56p.* The vector was transferred into the EHA105 strain (*Agrobacterium*).
