Comparative transcriptomics of cupuassu (Theobroma grandiflorum) offers insights into the early defense mechanism to Moniliophthora perniciosa, the causal agent of witches’ broom disease

Cupuassu (Theobroma grandiflorum) is a fruit tree native to the Amazon region, presenting high social and economic value. Besides, owing to its suitability for agroforestry cultivation, cupuassu is useful for the conservation of the Amazon Forest. Cupuassu plantations are severely affected by Moniliophthora perniciosa. Thus, to gain insights into resistance against M. perniciosa, transcriptomes of susceptible (SG) and resistant (RG) genotypes of cupuassu were analyzed at the early stage of infection using RNA sequencing. A total of 21,441 unigenes were identified, and differentially expressed genes were detected in intra- (440) and inter-genotype (301) analyses. Gene expression was altered at 24 h after inoculation (HAI) in SG. This alteration was prominent at 48 HAI in RG. These datasets allowed the identification of genes potentially involved in defense mechanisms. Phytohormone signature analysis revealed a significant effect of hormones on genotype responses. The present study is the first large-scale transcriptomic analysis of cupuassu.大花可可树（Cupuassu，Theobroma grandiflorum）是原产于亚马逊流域的果树，具备极高的社会与经济价值。同时，因其适配农林业种植模式，大花可可树还可助力亚马逊森林的保护工作。大花可可树种植园极易受到嗜松疫霉（Moniliophthora perniciosa）的严重为害。为此，为解析大花可可树对嗜松疫霉的抗病机制，本研究采用RNA测序（RNA sequencing）技术，对侵染早期的感病基因型（SG）与抗病基因型（RG）的转录组进行了分析。本研究共鉴定出21441个单基因簇，在基因型内比较（440个）与基因型间比较（301个）中均检测到差异表达基因。感病基因型在接种后24小时（HAI）即出现基因表达改变，而抗病基因型的基因表达变化在接种后48小时更为显著。本数据集助力鉴定出一批潜在参与植物防御机制的基因。植物激素特征分析显示，激素信号对两种基因型的抗病响应具有显著调控作用。本研究为全球首次针对大花可可树开展的大规模转录组学分析。