Analysis of Cf-12 Tomato Transcriptome Profile in Response to Cladosporium fulvum Infection with Hisat, StringTie and Ballgown

摘要

Nature Protocols introduced a new method of RNA-seq data processing with HISAT, StringTie and Ballgown, all of which are open-source software. HISAT aligns RNA reads to the genome; StringTie assembles the transcripts and computes their abundance, while Ballgown identifies differentially expressed genes and transcripts between samples. The software contained in these methods are flexible, accurate and efficient, making them convenient for researchers to use PC to analyze transcriptome data. The method provides a new way for RNA-seq from raw data reading to different expressions. The Cf gene is effective in resisting tomato leaf mold disease caused by Cladosporium fulvum. The C. fulvum-resistant tomato cultivars introduce Cf resistant genes identified from wild Solanum species. The C. fulvum pathogen has many physiological races, and newer physiological races have continued to evolve. Different from Cf genes such as Cf-2, Cf-4, Cf-5, and Cf-9, no C. fulvum physiological races virulent to Cf-12 carrying tomato lines have been identified. In order to better understand the molecular mechanisms involved in the Cf-12 gene resistance to C. fulvum, Hisat, StringTie and Ballgown were used to analyze the transcriptome changes at three different time stages of C. fulvum infection: 0 dpi (Cf12_A), 4 dpi (Cf12_B), and 8 dpi (Cf12_C). A total of 6446 differentially expressed genes (DEGs) between 4 and 0 dpi, and 7322 DEGs between 8 and 0 dpi were identified. Through GO and KEGG analysis, these DEGs were significantly highly enriched in plant pathogen interaction pathway and plant disease resistance-related pathway, indicating that these DEGs play important roles in C. fulvum defense response. GO analysis for the up-regulated genes showed that 25 terms were significantly regulated. Biological process categories such as salicylic acid metabolic pathway, and biosynthetic pathways for jasmonic acid and salicylic acid were highly enriched. Through KEGG pathway enrich analysis of the up-regulation, many up-regulated and DEGs were enriched in plant-pathogen interaction pathways and disease resistance-related pathways. These results indicate the resistance of Cf-12 tomato. We found 15 pathogenesis-related genes and 18 resistance protein genes in the DEGs. This study used novel methods and large data analysis theory to explore the mechanism of disease resistance of Cf-12 tomato, and it provides new insight on the molecular mechanism of Cf resistance to C. fulvum.