Transcriptome Analysis of Pepper-Phytophthora infestans Interaction Based on a Pipeline of a Simplified and Effective RNA-seq Analysis (PoRAS)

Crop productivity is threatened by a variety of pathogens. As a mean by which to solve this problem, research to identify resistance mechanisms and key factors through the use of plant-disease interaction transcripts is being actively conducted. The discovery of key factors through the next-generation sequencing (NGS) technique has been used in various studies, but the use of an optimized and simplified analysis pipeline is limited due to its complex and diverse programs. In this study, we present a pipeline of a simplified and effective RNA-seq analysis (PoRAS) for a transcriptome core analysis, with RNA-seq data of pepper-phytophthora infestans interaction global gene profiling, differential gene expression (DEG), and a gene set enrichment analysis (GSEA) then performed to validate the PoRAS. Data preprocessing and quality checks were conducted for a total of 39 transcripts using the established transcriptome analysis pipeline, and it was confirmed that 84.87–92.38% of high-quality sequences remained in each dataset. Subsequently, 2,594 DEGs were obtained through a DEG analysis, and the function of the gene cluster was confirmed through a GSEA. This led to the confirmation that the functions of the defense response, response to a biological stimulus, and the recognition of pollen appeared most significantly. These results suggest that PoRAS can be a useful tool for basic and core analyses to find and identify key genetic factors from a large amount of RNA-seq data. Through this, the analysis pipeline presented in this study, PoRAS, is deemed feasible as a strategy to secure key genetic factors if used to conduct basic to core analysis stages targeting a large amount of RNA-seq information.