Integrative analysis of the transcriptome and metabolome reveals the response mechanism to tomato spotted wilt virus

Tomato spotted wilt virus (TSWV) is an important virus that has rapidly spread throughout the world. TSWV seriously hinders the production of tomato (Solanum lycopersicum) and other plants. In order to discover more new genes and metabolites related to TSWV resistance in tomato plants, the genes and metabolites related to the resistance of tomato plants inoculated with TSWV were identified and studied herein. The tomato TSWV-resistance line YNAU335 (335) and TSWV-susceptible lines NO5 and 96172I (961) were used as the transcriptome and metabolome research materials. Transcriptomic and metabolomic techniques were used to analyze the gene and metabolite response mechanisms to TSWV inoculation. A total of 3 566, 2 951, and 2 674 differentially expressed genes (DEGs) were identified in lines 335, NO5, and 961, respectively. Meanwhile, 208, 228, and 273 differentially accumulated metabolites (DAMs) were identified in lines 335, NO5, and 961, respectively. In line 335, the number of DEGs was the highest, but the number of DAMs was lowest. Furthermore, 903 DEGs and 94 DAMs were common to the response to TSWV in the three inbred lines. The 903 DEGs and 94 DAMs were mainly enriched in the plant hormone signal transduction and flavonoid synthesis pathways. In addition, many nucleotide-binding site-leucine-rich repeat genes and transcription factors were found that might be involved in the TSWV response. These results provide new insights into TSWV resistance mechanisms.