Spore Germination of the Obligate Biotroph Spongospora subterranea: Transcriptome Analysis Reveals Germination Associated Genes

Abstract

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.

In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host–Pathogen Interaction

“…The dependence of spore germination on transcription and translation has been demonstrated in many pathogens [ 58 , 59 , 60 ]. This finding aligned with the observed upregulation of transcription and protein synthesis in our previous in vitro analysis of transcriptome and proteome of S. subterranea during the germination of resting spores [ 18 , 19 ]. Therefore, transcription and translation may be induced upon the activation of resting spores both in planta and in vitro.…”

“…The in planta transcriptomes and proteomes of S. subterranea obtained in this study were compared to our previous in vitro transcriptome [ 18 ] and proteomic [ 19 ] studies of S. subterranea . The number of identified genes was significantly higher in the in planta analysis of S. subterranea transcriptome ( Figure 6 A, left).…”

“…The list of differentially expressed genes (DEGs) was filtered with a cut-off for a false discovery rate (FDR) of 0.05. The RNA-seq data were further validated using qRT-PCR as described before [ 18 ]. The primer sequences were listed in Supplementary Table S1 .…”

“…To understand the biology and virulence of obligate biotrophic plant pathogens, a comprehensive analysis of the transcriptome and proteome of these pathogens is a priority. We have researched the transcriptome [ 18 ] and proteome [ 19 ] dynamics of S. subterranea during the germination of resting spores using an in vitro model. However, to better understand the complex life cycle of the obligate biotrophic pathogens inside their host, a comparable effort to analyse the in planta transcriptome and proteome of S. subterranea during root infection is required.…”

Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant–Pathogen Interactions

“…An understanding of how pathogens and plants recognize each other and how they communicate pre- and post-infection is crucial in this field of investigation. The increase in genomic and transcriptome studies has advanced the understanding of the pathogenicity strategies employed by pathogens and the immune responses in plants [ 2 , 3 , 4 , 5 ]. However, these approaches have limitations and cannot monitor post-transcriptional processes [ 6 ].…”