*3.3. Structure of Hsf and Hsp Genes and Conserved Motifs of Hsf and Hsp Proteins in Eggplant*

To obtained further insights into the structural diversity of *Hsf* and *Hsp* genes in eggplant, we used the Multiple Expectation maximization for Motif Elicitation (MEME) [27] to predict the conserved motifs shared among the related proteins within these families. In each family, 20 putative motifs were identified. The details of these motifs are listed in Tables S8–S13. Most of the closely related members in the phylogenetic tree shared common motif compositions.

The exon/intron structures of eggplant *Hsf* and *Hsp* members were analyzed based on their coding sequences and the corresponding genome sequences. The eggplant *Hsfs* shared highly conserved exon/intron structures with 0–3 intron phases (Figure 1A). The intron phases were remarkably well conserved among family members. Most of the eggplant *sHsps* did not contain introns and only a few had 1–3 introns (Figure 1B). Interestingly, in the *Hsp60* family, two members, *SmCpn60-8* and *SmHsp60-3,* had no introns in their coding regions, while the other eggplant Hsp60s contained several introns (1–22) (Figure 1C). In the *Hsp70* family, cytosolic *Hsp70s* had 0–13 introns, ER-localized BIPs had 4–7 introns, mitochondrion-localized *mtHsc70s* had 0–4 introns and chloroplast-localized *cpHsc70s* had 6 introns, while truncated *Hsp70ts* had no introns (Figure 2A). With the exception of *SmHsp90-1.1*, each *Hsp90s* member contained 1–17 introns (Figure 2B). The number of exons and introns of *Hsp100* family members differed greatly. For example, *SmHsp100-ClpX1* contained up to 16 introns, but *SmHsp100-ClpB3* and *SmHsp100-ClpC3* only had 4 introns (Figure 2C).

**Figure 1.** Phylogenetic relationships, gene structures and motif compositions of *Hsf, sHsp* and *Hsp60* family members in eggplant. Multiple alignment of the Hsf (**A**), sHsp (**B**) and Hsp60 (**C**) proteins from eggplant (Sm) was performed with MEGA 5.0 using the neighbor-joining (NJ) method with 1000 bootstrap replicates (left panel). A schematic representation of conserved motifs (obtained using MEME) in the Hsf and sHsp proteins is displayed in the middle panel. Different motifs are represented by differently colored boxes. Details of the individual motifs are in Tables S8–S10. Exon/intron structures of the *Hsf* and *sHsp* genes are shown in the right panel. Green boxes represent exons and black lines represent introns.

**Figure 2.** Phylogenetic relationships, gene structures and motif compositions of the Hsp70, Hsp90 and Hsp100 family members in *S. melongena* (Sm). Multiple alignment of the Hsp70 (**A**), Hsp90 (**B**) and Hsp100 (**C**) proteins from *S. melongena* (Sm) was performed with MEGA 5.0 using the neighbor-joining (NJ) method with 1000 bootstrap replicates (left panel). A schematic representation of conserved motifs (obtained using MEME) in the Hsp70 (**A**), Hsp90 (**B**) and Hsp100 (**C**) proteins is displayed in the right panel. Different motifs are represented by differently colored boxes. Details of the individual motifs are in Tables S11–S13. The exon/intron structures of the Hsp70 (**A**), Hsp90 (**B**) and Hsp100 (**C**) genes are shown in the middle panel. Green boxes represent exons and black lines represent introns.
