De novo transcriptome sequencing of rough lemon leaves (Citrus jambhiri Lush.) in response to Plenodomus tracheiphilus infection

Mal secco is one of the most severe diseases of citrus, caused by the necrotrophic fungus Plenodomus tracheiphilus that is widespread in different Mediterranean countries. With the main aim of identifying candidate genes involved in the response of citrus plants to “Mal secco”, we performed a de novo transcriptome analysis of rough lemon seedlings subjected to artificial inoculation of P. tracheiphilus in comparison with plants inoculated with water. The analysis of Differential Expressed Genes (DEGs) highlighted a sharp response triggered by the pathogen as a total of 4,986 significant DEGs (2,865 genes up-regulated and 2,121 down-regulated) have been revealed. The analysis of the most significantly enriched KEGG pathways indicated that a crucial role in the plant response to the fungus is played by genes involved in “Plant hormone signal transduction”, “Phenylpropanoid biosynthesis” and “Carbon metabolism”. The main findings of this work are that under fungus challenge, the rough lemon genes involved both in the light harvesting and the photosynthetic electron flow were significantly down-regulated, thus probably inducing a shortage of energy for cellular functions. Moreover, the systemic acquired resistance (SAR) was activated through the induced salicylic acid cascade. Interestingly, RPM1 interacting protein 4, an essential positive regulator of plant defense, and BIR2, which is a negative regulator of basal level of immunity, have been identified thus representing useful targets for molecular breeding. Overall design: Examination of Citrus jambhiri response to Plenodomus tracheiphilus infection. Six leaf samples coming from six different Citrus jambhiri plants have been analyzed. Three samples come from leaves wounded and inoculated with water, corresponding to three biological replicates of the control thesis. Three samples come from leaves wounded and inoculated with a suspension of Plenodomus tracheiphilus PT10 strain phialoconidia, corresponding to three biological replicates of the treatment thesis.

"Mal secco"是柑橘最严重的病害之一，由死体营养型真菌（necrotrophic fungus）Plenodomus tracheiphilus引起，该真菌在多个地中海国家广泛分布。本研究旨在鉴定参与柑橘植株对"Mal secco"病害应答的候选基因，对经人工接种Plenodomus tracheiphilus的粗柠檬（Citrus jambhiri）幼苗开展了从头转录组分析，并以接种无菌水的植株作为对照。差异表达基因（Differential Expressed Genes, DEGs）分析结果显示，该病原触发了强烈的宿主应答，共鉴定得到4986个显著DEGs，其中2865个基因上调表达，2121个基因下调表达。对显著富集的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路的分析表明，参与"植物激素信号转导""苯丙烷类生物合成"以及"碳代谢"的基因在植株应对该真菌的过程中发挥关键作用。本研究的核心发现为：在真菌侵染胁迫下，粗柠檬中参与光捕获及光合电子传递的基因均显著下调，这可能会导致细胞功能所需的能量供应不足。此外，通过激活水杨酸信号级联反应，植株的系统获得性抗性（systemic acquired resistance, SAR）得以启动。值得注意的是，本研究鉴定得到了RPM1互作蛋白4（RPM1 Interacting Protein 4）——一种植物防御的关键正调控因子，以及基础免疫水平的负调控因子BIR2，二者均可作为分子育种的潜在靶点。整体实验设计：检测粗柠檬对Plenodomus tracheiphilus侵染的应答反应。本研究共分析6份叶片样本，均来自6株不同的粗柠檬植株。其中3份样本取自经伤口处理并接种无菌水的叶片，对应对照组的3个生物学重复；另外3份样本取自经伤口处理并接种Plenodomus tracheiphilus PT10菌株分生孢子悬浮液的叶片，对应处理组的3个生物学重复。