Transcriptome analysis of the response mechanism of Alternaria alternata to in vitro L-cysteine treatment

L-cysteine (Cys) has been reported to significantly suppress the in vitro growth of Alternaria alternata and disrupt its cell wall and membrane integrity. However, the precise mechanisms underlying this inhibitory effect remain unclear. To identify the specific genes and pathways influenced by Cys treatment, the transcriptomic profile of A. alternata following 2 d of incubation was characterized using RNA sequencing. A total of 9, 982 genes were identified, of which 1, 350 genes exhibited differential expression between the control and Cys-treated samples. These differentially expressed genes were predominantly enriched in functional categories such as transmembrane transporter activity, glycolysis metabolism, ribosome biogenesis, as well as Cys and reduced gluthathione metabolic pathways. Meanwhile, it was observed that Cys significantly influenced pentose phosphate pathway and dihydroxyphenylalanine (DOPA) melanin synthesis pathways. Furthermore, RT-qPCR analysis confirmed that Cys treatment distinctly up-regulated the relative expression levels of AaRio2, AaNob1, AaNop1, AaNmd3, AaLsg1, AaSdo1, AaCDO, AaCSE, AaGCL, AaGS, AaGST, and AaGR, while simultaneously down-regulating the relative expression levels of AaTYR and AaOAS-TL. Altogether, Cys treatment suppressed transmembrane transporter activity, glycolytic metabolism, and DOPA melanin synthesis in A. alternata, thereby promoting ribosome biogenesis, the pentose phosphate pathway, and Cys metabolism. This enhancement activated the fungal detoxification and defense mechanisms.