*2.1. Plant Materials and Growth Conditions*

The *S. lycopersicum* cultivar 'Diana' was grown at the experimental farm of the Shandong Facility Horticultural Laboratory, Weifang, Shandong Province, China. Tomato seeds were planted in plug plates (Wei Nong Company, Taizhou, China). One month later, we treated the *S. lycopersicum* plants with different concentrations of PHBA (0 mmol/L, 15 mmol/L, and 30 mmol/L) for 2 days. Then, the leaves from the middles of the plants were collected as samples. Specifically, the samples for the CK, T1, and T2 treatments corresponded to the 0 mmol/L, 15 mmol/L, and 30 mmol/L concentrations of PHBA, respectively (Figure 1A). We collected leaf samples from 60 individual tomato seedlings and stored them at −75 ◦C in an ultra-low temperature freezer for the following experiments.

#### *2.2. RNA Sequencing and Identification of lncRNAs*

Total RNA was extracted from the leaf samples for the different PHBA treatments described above using the MagMAX Plant RNA Isolation Kit (Thermo Fisher Scientific, Carlsbad, CA, USA). RNA quality was measured with a Thermo Scientific NanoDrop 2000 system (Thermo Fisher Scientific, USA), and RNA integrity was examined with an Agilent 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA, USA) [42]. RNAs with integrity numbers greater than 7 were selected for strand-specific RNA-seq library construction. First, ribosomal RNAs were removed from the total RNAs using the plant Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA). A strand-specific RNA-seq library was constructed with the Ribo-Zero RNA fraction via the Illumina TruSeq RNA Library Preparation Kit v2 and sequencing on an Illumina HiSeq 4000 instrument.

**Figure 1.** Characteristics of lncRNAs identified in *S. lycopersicum* leaves. (**A**) 'Diana' of *S. lycopersicum* under different treatments of PHBA (scale bar represents 5 cm). (**B**) Length distribution of lncR-NAs. (**C**) LncRNA expression levels. (**D**) The numbers of lncRNAs and PGs expressed in different treatments.

After removing adaptors and low-quality reads from raw reads using Trimmomatic [43], 1,003,711,588 paired-end clean reads were produced (111,523,510 on average for each sample). They were subjected to de novo transcript assembly using Trinity (v2.8.4, Manfred G. Grabherr, Cambridge MA, USA), with strand-specific RNA-Seq read orientation [44]. Duplicates were then removed from the assembled transcripts using CD-HIT (v4.7, Limin Fu, La Jolla CA, USA) with default parameters [45]. Finally, we obtained 82,126 unigenes longer than 200 bp for lncRNA screening. The lncRNA identification process is shown in Figure S1. To improve the accuracy of lncRNA detection, three software programs, RNAplonc (v1.0, Tatianne da Costa Negri, São Paulo, Brazil) [46], PLncPRO (v1.1, Urminder Singh, New Delhi, India) [47], and FEELnc (v0.1.1, Valentin Wucher, Rennes, Cedex, France) [48], with default parameters, were employed to identify lncRNAs. The lncRNAs obtained with these three tools were compared to obtain the shared pre-lncRNA candidates. To further rule out the possibility that the pre-lncRNAs were from coding genes, these pre-lncRNAs were blasted against coding DNA sequences of *S. lycopersicum* (SL.3.0) using BLAT v36 × 2 software [49] with an E-value of 10<sup>−</sup>5. The filtered lncRNA candidates were then localized to the *S. lycopersicum* reference genome using BLAT to remove repeat sequences, so we could eliminate ones that had more than nine positions and which were considered to be repeats in the genome. Eventually, we identified highly reliable putative lncRNAs in *S. lycopersicum*.
