*2.6. RNA Isolation and Sequencing*

Total RNA was extracted from control samples on days 0 and 14 and from CS samples on day 14 using the RNAprep Pure Plant Kit (Tiangen Biotech Co., Ltd., Beijing, China). Agarose gel electrophoresis was used to evaluate the RNA integrity. RNA sequencing (RNA-Seq) was then conducted by BmK Biotechnology Co., Ltd. (Beijing, China). Adapter sequences and low-quality sequences were then filtered out to ensure that all downstream analyses were conducted using clean and high-quality data. The hisat2 software was then used to map the data to the wild sweet potato reference genome ( http://sweetpotato.plantbiology.msu.edu/ (accessed on 15 October 2020)). The hisat2 software uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a wholegenome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments [19]. Functional annotation, cluster analysis, proteinprotein interaction network analysis, and more in-depth mining analysis were conducted thereafter.
