Messenger RNA-seq data of tomato lines affected in the LTP2 gene. RNA isolation To isolate RNA, plant tissues were flash frozen in liquid nitrogen immediately after harvesting and stored at −80°C prior to RNA extraction. Frozen pellets were grounded by using a mortar and pestle before immersion in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified into two separate fractions (>200 nt and <200 nt) using the miRNeasy Mini kit (Qiagen). For the >200 nt RNA an on-column treatment was included using the RNase-free DNase set (Qiagen). mRNA sequencing protocol A poly-A enrichment was performed on the >200 nt RNA fraction using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). RNA-Seq libraries were generated according to the manufacturers’ protocols using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) (New England BioLabs). The size distribution of the libraries with indexed adapters was assessed using a 2200 TapeStation System with Agilent D1000 ScreenTapes (Agilent Technologies). The libraries were quantified on a QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific) using the NEBNext Library Quant Kit for Illumina (New England BioLabs) according to the instructions of the manufacturer. The libraries were clustered and sequenced (75 bp) on a NextSeq 550 Sequencing System (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina). The sample list can be found in list_of_samples.csv.