*3.2. Evolutionary Analysis of the bHLH Genes*

The phylogenetic tree was constructed using the full-length sequences of the PebHLH and AtbHLH proteins (Figure 1). The PebHLHs could be divided into eighteen groups according to the evolutionary relationship. In groups 1 to 18, the largest number of *PebHLHs* was in group 1, with 11 members, and the smallest number was two in group 9. The number of PebHLH members in the remaining groups was between 4–10. The known *AtbHLHs* were then used to infer the hypothetical homologous members of *PebHLHs*. Among group 1–6, *PebHLH11/101/80/31/42/88/98/41/18/108/54/46/13/66/44/14* exhibited the closest relationship with At3G50330.1, At3G19500.1, At2G31730.1, At2G43010.5, At1G73830.1, At1G05805.1, At1G51140.1, At4G29100.1, At2G43140.2, At1G27660.1, At1G29950.2, At5G65320.1, respectively. Among groups 7–12, *PebHLH85/112/62/102/38/97/92/100/47/61/19/52/45* was the most homogeneous gene of At4G30980.1, At4G00480.2, At5G51790.2, At2G22760.1, At2G31280, 1At3G23210.1, At2G16910.1, At5G57150.2, At1G32640.1, At2G24260.2, At4G36060.2, At3G19860.3, At5G56960.2, respectively. Among group 13–18, *PebHLH57/43/91/5/12/69/99/ 26/114/84/22/95*, was the best orthologous match of At1G18400.1, At4G21340.1, At5G08130.3, At3G24140.1, At1G71200.1, At4G30410.1, At1G25330.1, At5G62610.1, At2G46510.1, At5G50915.1, At5G61270.2, respectively.

**Figure 1.** Phylogenetic relationship of bHLHs between passion fruit and *Arabidopsis*. The different colors of the outer circles represented groups 1–18. Pe and At are abbreviations of passion fruit and *Arabidopsis*, respectively.

#### *3.3. Analysis of Gene Structure and Conserved Motifs*

A total of 10 conserved motifs in *PebHLHs* were predicted (Figure 2). Although most members have two to four motifs, few members have only one motif; for example, *PebHLH*26*/48/91* only has motif one. *PebHLH30/38/41/43/52* only has motif two. Specifically, most members contain motifs 1 and 2, such as 111 members contain motif 1, and 114 members contain motif 2. In addition, 30 members contain motif 3, 38 members contain motif 4, 14 members contain motif 5, 17 members contain motif 6, and 4 members contain motif 7.

The exon and intron organization of *PebHLH* gene DNAs were analyzed. The bulk of members had the structure of 5 and 3 UTR (untranslated region), and 18 only had exons and introns. Among them, nine members (*PebHLH14/27/31/48/55/81/95/98/111*) only had 5 UTR, and 23 members only had 3 UTR. The number of exons was between 2–11(Figure 2).
