*3.7. Collinearity Analysis of PebHLHs*

All *PebHLH* genes were found to be displayed on chromosomes except for *PebHLH111- 117*. There are 68 collinearity pairs that can be found. Most *PebHLHs* were found with one paralogous gene (Figure 6A).

The collinearity analysis among species was performed, and respectively, there were 12,406, 3118, and 25,224 genes in *Arabidopsis*, rice, and poplar, having a collinearity relationship with passion fruit. Among them, members of the PebHLH family had 91, 31, and 170 connections with *Arabidopsis*, rice, and poplar, respectively (Figure 6B). This result indicates that the homologous relationship between passion fruit and poplar is the closest, followed by *Arabidopsis* and rice.

Out of the 117 members, 27 and 22 genes had two and one homologous genes with the other three species, respectively. Other members have three to eight homologous genes. Among them, *PebHLH56* has 9 homologous genes (At1G01260.3, At1G63650.3, At2G46510.1, At4G00870.1, PNT03691, PNT03984, PNT45271, PNT50177, PNT53769) in collinear connections with *Arabidopsis* and poplar. In addition, 18 genes (*PebHLH27/28/33/35/36/40/46/58/61/ 67/78/91/97/98/99/109/110/115*) had one orthologous gene in rice.

**Figure 4.** The cis-acting element analysis of 2000 bp promoter upstream of *PebHLH* genes. Functional descriptions of cis-acting elements were labeled by different colors.

**Figure 5.** Protein interaction networks prediction of PebHLH. The outer blue circles indicate PebHLH proteins, and the inner red circles indicate other proteins in the reciprocal relationship. Interacting relationships are indicated by straight gray lines.

**Figure 6.** The synteny analysis of bHLHs of passion fruit genomes (**A**) and with other species (**B**). The red line represents the *PebHLH* gene pair, and the blue lines represent homologous gene pairs. Pe, Os, At, and Pt represent passion fruit, rice, *Arabidopsis*, and poplar, respectively.
