Transcriptomic Analyses Provide Insights into Plant-Viroid Interactions

Plants have evolved elegant regulatory programs that can rapidly elicit the expression of defense-related genes in response to pests and pathogens, such as viroids. These defense-related genes include small RNAs, long noncoding RNAs, protein-coding mRNAs, etc. Transcriptomic analyses provide a powerful toolset to uncover those genes that have altered expression profiles in viroid-infected plants. This chapter introduces the basic concept and a brief history of transcriptomic analysis as well as its application in understanding plant-viroid interactions. This chapter intends to focus on introducing the background and methodology of transcriptomic analyses instead of providing a comprehensive literature review. While the chapter focuses on the description of the most popular RNA deep sequencing analyses, readers are referred to other resources in the Further Reading section to gain a better grasp on small RNA deep sequencing, degradome RNA deep sequencing, etc.