Supplementary file 1_Transcriptome profiling reveals tissue-wide gene expression in chili pepper (Capsicum annuum L.) under infection by Phytophthora capsici.docx

Phytophthora blight, manifested by root, stem, and fruit rot, caused by the oomycete Phytophthora capsici, is an important disease affecting Chili pepper production globally. RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs) and shared genetic resistance mechanisms across different tissues upon infection by the pathogen. RNA-seq revealed the dynamic transcriptome of leaf, stem, and root tissues from resistant (R; CM-334) and susceptible (S; Early Jalapeño) varieties under different times of infection by P. capsici. There were 149,531 differentially expressed genes (DEGs) from 39 different R vs. S, time vs. time, and tissue vs. tissue comparisons. A total of 75,520 DEGs (51%) showed higher expression, whereas 74,011 (49%) demonstrated lower expression across all tissues and times of post-inoculation. The total number of DEGs with higher expression for the different tissue samples decreased across times of post-inoculation, where the 72h post-inoculation showed the least number of genes. The roots generally showed a higher number of DEGs compared to the stems and the leaves. Network analyses of DEGs demonstrated that genes with functions related to defense response to fungal infection were also involved with carbohydrate metabolism and ADP binding. Genes related to immune response to fungal infection and amino acid metabolism (e.g., homoserine kinase activity) showed higher gene expression across all times of infection and tissue samples. Chili pepper transcriptome under P. capsici infection provides evidence of shared gene expression across multiple tissues which can be leveraged for breeding and selection for broad-spectrum resistance in current Capsicum germplasm.

由卵菌辣椒疫霉（Phytophthora capsici）引发的疫霉病（Phytophthora blight）以根、茎和果实腐烂为典型症状，是全球范围内严重危害辣椒生产的重要病害。本研究通过RNA测序（RNA-seq），旨在鉴定病原菌侵染后不同组织间的差异表达基因（differentially expressed genes, DEGs）以及共享的遗传抗病机制。RNA-seq解析了抗病（R；CM-334）与感病（S；Early Jalapeño）品种的叶、茎、根组织在辣椒疫霉不同侵染时间点下的动态转录组。本研究通过39组不同的抗病vs感病、不同时间点vs不同时间点以及不同组织vs不同组织的比较，共鉴定出149531个差异表达基因（DEGs）。在所有组织和接种后时间点中，共有75520个DEGs（占比51%）表达上调，74011个DEGs（占比49%）表达下调。不同组织样本的上调DEGs总数随接种后时间推移逐渐减少，其中接种后72小时（72h）的上调基因数量最少。总体而言，根组织的DEGs数量显著多于茎和叶组织。对DEGs的共表达网络分析表明，参与真菌侵染防御反应的基因同时也参与了碳水化合物代谢与腺苷二磷酸（ADP）结合过程。与真菌侵染免疫反应及氨基酸代谢（如高丝氨酸激酶活性）相关的基因，在所有侵染时间点和组织样本中均呈现高表达水平。辣椒受辣椒疫霉侵染后的转录组数据，为多组织间共享的基因表达模式提供了研究证据，可应用于当前辣椒属（Capsicum）种质资源的广谱抗病育种与抗性筛选工作。