*3.4. Prediction of TTPGs of lncRNAs*

Using RNAplex software, 989 lncRNAs and 1765 TPGs in 5659 gene pairs were predicted to be trans-regulated (Table S10). Among the 989 lncRNAs, 30.9% of them targeted only one gene, 0.4% of which targeted more than 100 genes (Figure 3B). Among the 1765 targets, 697 (39.5%) were trans-regulated by one lncRNA; in contrast, 82 targets (4.6%) were targeted by more than 10 lncRNAs (Figure 3B).

Using WGCNA, 989 lncRNAs and their 1765 TTPGs were divided into 11 modules (Figure 4B). The proportions of lncRNAs ranged from 11.1% in M14 to 67.1% in M15, with an average of 35.9% in these modules (Table S6). Except for M15, M19, M20, M21, and M23, remarkable GO terms were verified in most modules, with a range from 106 in M15 to 6 in M23 (Table S11). Distinguishable expression patterns were found in all of the modules (Figure 7). For example, genes in M16 and M19 were extremely highly expressed in plants undergoing the T2 treatment (Figure 7) and were annotated as being associated with the following terms: reactive oxygen species metabolic process, antibiotic catabolic process, and hydrogen peroxide catabolic process (Figure 8). Regulatory networks that were widely interconnected between mRNAs and lncRNAs were found in all modules of trans-regulatory activity (Data S1).

**Figure 7.** Expression patterns of lncRNAs and TTPGs in different modules.

**Figure 8.** GO annotations of lncRNAs and TTPGs in Module 16 (**A**) and Module 19 (**B**).

A total of 335 trans-acting lncRNAs were highly correlated with their 633 targets (Spearman coefficient rho (rs) > 0.9) (Table S12); 681 gene pairs were positively correlated, while 554 pairs were negatively. The expression patterns of the targets indicated that 1035 were upregulated and that 730 were downregulated in at least one treatment (Table S13).

#### *3.5. Similarity Alignment and Conservation Analysis of lncRNAs in S. lycopersicum and Arabidopsis thaliana*

As a model plant and close species of *S. lycopersicum*, *Arabidopsis thaliana* was used to analyze the lncRNA similarities between them. Although there were 65,178 lncRNAs in *S. lycopersicum*, only 98 had homologs in *Arabidopsis thaliana* (Table S14). Expression analysis revealed that these 98 lncRNAs were affected by the PHBA treatments (Figure 9).

**Figure 9.** Expression patterns of *S. lycopersicum* lncRNAs with homologs in *Arabidopsis thaliana*.
