The <i>Rhizoctonia solani</i> AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (<i>Lactuca sativa</i> L.)

<div><p>The necrotrophic pathogen <i>Rhizoctonia solani</i> is one of the most economically important soil-borne pathogens of crop plants. Isolates of <i>R</i>. <i>solani</i> AG1-IB are the major pathogens responsible for bottom-rot of lettuce (<i>Lactuca sativa</i> L.) and are also responsible for diseases in other plant species. Currently, there is lack of information regarding the molecular responses in <i>R</i>. <i>solani</i> during the pathogenic interaction between the necrotrophic soil-borne pathogen and its host plant. The genome of <i>R</i>. <i>solani</i> AG1-IB (isolate 7/3/14) was recently established to obtain insights into its putative pathogenicity determinants. In this study, the transcriptional activity of <i>R</i>. <i>solani</i> AG1-IB was followed during the course of its pathogenic interaction with the host plant lettuce under controlled conditions. Based on visual observations, three distinct pathogen-host interaction zones on lettuce leaves were defined which covered different phases of disease progression on tissue inoculated with the AG1-IB (isolate 7/3/14). The zones were defined as: Zone 1—symptomless, Zone 2—light brown discoloration, and Zone 3—dark brown, necrotic lesions. Differences in <i>R</i>. <i>solani</i> hyphae structure in these three zones were investigated by microscopic observation. Transcriptional activity within these three interaction zones was used to represent the course of <i>R</i>. <i>solani</i> disease progression applying high-throughput RNA sequencing (RNA-Seq) analysis of samples collected from each Zone. The resulting three transcriptome data sets were analyzed for their highest expressed genes and for differentially transcribed genes between the respective interaction zones. Among the highest expressed genes was a group of not previously described genes which were transcribed exclusively during early stages of interaction, in Zones 1 and 2. Previously described importance of up-regulation in <i>R</i>. <i>solani</i> agglutinin genes during disease progression could be further confirmed; here, the corresponding genes exhibited extremely high transcription levels. Most differentially higher expressed transcripts were found within Zone 2. In Zone 3, the zone with the strongest degree of interaction, gene transcripts indicative of apoptotic activity were highly abundant. The transcriptome data presented in this work support previous models of the disease and interaction cycle of <i>R</i>. <i>solani</i> and lettuce and may influence effective techniques for control of this pathogen.</p>