RNA-Seq Analysis of Phytophthora capsici

For RNA sequencing, mycelium samples were collected from the V8 medium after 4 days of culturation. Total RNA was isolated from the samples using Trizol reagent (Invitrogen) and an RNA Clean-Up Kit-5 (Zymo Research, R1016), following the manufacturer's instructions. The extracted mRNA was used to construct the cDNA library, and the library construction was sequenced on an Illumina Hiseq 4000 Platform (Lc-Bio Technologies, Hangzhou, China). The preprocessed RNA-Seq reads were mapped to the reference genome of P. capsici strain LT1534 (https://mycocosm.jgi.doe.gov/Phyca11/Phyca11.home.html) [59 (link)] using the HISAT package [60 (link)], and the mapped reads of each sample were assembled using the StringTie method [61 (link)]. The DEGs were identified from RNA-Seq data with the cut-off of the corrected p-value < 0.05, using log2foldchange greater than or equal to 1 as a threshold. Analyses of the biological information of DEGs were performed using an online database (http://geneontology.org/); analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) was performed using an online database (www.genome.jp/kegg) as a reference.