Data_Sheet_1_Spore Germination of the Obligate Biotroph Spongospora subterranea: Transcriptome Analysis Reveals Germination Associated Genes.PDF

For soilborne pathogens, germination of the resting or dormant propagule that enables persistence within the soil environment is a key point in pathogenesis. Spongospora subterranea is an obligate soilborne protozoan that infects the roots and tubers of potato causing root and powdery scab disease for which there are currently no effective controls. A better understanding of the molecular basis of resting spore germination of S. subterranea could be important for development of novel disease interventions. However, as an obligate biotroph and soil dwelling organism, the application of new omics techniques for the study of the pre-infection process in S. subterranea has been problematic. Here, RNA sequencing was used to analyse the reprogramming of S. subterranea resting spores during the transition to zoospores in an in-vitro model. More than 63 million mean high-quality reads per sample were generated from the resting and germinating spores. By using a combination of reference-based and de novo transcriptome assembly, 6,664 unigenes were identified. The identified unigenes were subsequently annotated based on known proteins using BLAST search. Of 5,448 annotated genes, 570 genes were identified to be differentially expressed during the germination of S. subterranea resting spores, with most of the significant genes belonging to transcription and translation, amino acids biosynthesis, transport, energy metabolic processes, fatty acid metabolism, stress response and DNA repair. The datasets generated in this study provide a basic knowledge of the physiological processes associated with spore germination and will facilitate functional predictions of novel genes in S. subterranea and other plasmodiophorids. We introduce several candidate genes related to the germination of an obligate biotrophic soilborne pathogen which could be applied to the development of antimicrobial agents for soil inoculum management.

对于土传病原菌而言，能在土壤环境中持续存活的休眠繁殖体萌发，是致病过程的关键环节。马铃薯粉痂病菌（Spongospora subterranea）是一类专性土传原生生物，可侵染马铃薯的根系与块茎，引发根部病害与粉痂病，目前尚无有效防治手段。深入解析该菌休眠孢子萌发的分子机制，对开发新型病害防控策略具有重要价值。然而，作为专性活体营养型生物与土壤栖息生物，利用新兴组学技术（omics techniques）研究马铃薯粉痂病菌的侵染前过程仍存在诸多阻碍。本研究采用RNA测序（RNA sequencing）技术，在体外模型中分析了马铃薯粉痂病菌休眠孢子向游动孢子转变过程中的基因表达重编程事件。从休眠孢子与萌发孢子样本中，每个样本平均获得超过6300万条高质量读段。通过结合基于参考基因组的转录组组装与从头转录组组装策略，共鉴定得到6664个单基因簇（unigenes）。随后通过BLAST比对（BLAST search），基于已知蛋白序列对鉴定得到的单基因簇进行功能注释。在5448个完成注释的基因中，有570个基因在马铃薯粉痂病菌休眠孢子萌发过程中呈现差异表达，其中显著差异表达基因主要富集于转录与翻译、氨基酸生物合成、物质转运、能量代谢、脂肪酸代谢、应激响应以及DNA修复等生理过程。本研究生成的数据集为解析孢子萌发相关的生理过程提供了基础认知，将助力马铃薯粉痂病菌及其他根肿菌（plasmodiophorids）中新基因的功能预测。本研究筛选得到多个与专性活体营养型土传病原菌萌发相关的候选基因，可应用于土壤接种体管理相关抗菌剂的开发。