Transcriptome Sequencing Provides Insights into Understanding the Infection Mechanism of Alternaria solani on Potato

Abstract

Abstract Background Alternaria solani (A. solani), the main pathogen of potato early blight, causes serious yield reduction every year. However, the molecular interaction between A. solani and its host, potato, is largely unknown. In this study, a deep RNA-sequencing approach was applied to gain insights into the pathogenesis of A. solani. At 3, 4, and 5 days post inoculation (dpi), RNA samples from the susceptible potato cultivar Favorita infected by A. solani strain HWC-168, were sequenced and utilized for transcriptome analysis. Results A total of 4430 (2167 up-regulated, 2263 down-regulated), 4736 (2312 up-regulated, 2424 down-regulated), and 5043 (2411 up-regulated, 2632 down-regulated) genes were differentially expressed at 3, 4 and 5 dpi, respectively. KEGG enrichment analysis showed that the genes of amino acid metabolism, glucose metabolism, and enzyme activity were significantly expressed at the late infection stage. Correspondingly, the symptoms developed rapidly during the late stage infection of A. solani. In addition, the short time-series expression miner (STEM) assay was conducted to analyze the gene expression patterns of A. solani and it was found that profile 17 and 19 showed significant changing trends at 3, 4 and 5 dpi. Both profiles especially profile 17 contained a large number of enzymatic proteins, including transferases, oxidoreductases, hydrolases and carbohydrate-active enzymes (CAZYmes), which may play important roles in the late process of fungal infection. Furthermore, we screened possible candidate effectors by an adopted pipeline and found 137 differentially expressed small secreted proteins, which included some enzymes and unknown function proteins. Conclusions Collectively, the data presented in this study showed that amino acid metabolism, and glucose metabolism pathways may be the key metabolic pathways and these specific enzymes were important at the late stage of A. solani infection. These results contributed to the establishment of a broader knowledge of the pathogenesis of A. solani to potato at the transcriptional level and provided clues for determining the effectors of A. solani.