DDD Conference

Dr. Shikha Verma

Understanding Self/Nonself and Relative Recognition in Plants using Integrated Transcriptomics and Metabolomics Analysis

Ben Gurion University of the Negev, Israel


Competition is the major factor affecting the performance of naturally growing plants through direct and indirect interactions. The mechanism behind self and nonself and different degrees of relatedness recognition is still unknown. Hence, to gain insight into the molecular mechanisms and metabolic process underlying identity recognition, we investigated the Solanaceae family, tomato (Solanum lycopersicum L.) and bell pepper (Capsicum annum. L.) with all possible combinations, i.e., tomato (self), tomato-tomato (nonself, closely related), tomato-bell (nonself, far related), bell (self) and bell-bell (nonself, closely related) under control condition. To determine the metabolomic regulatory mechanisms, root tissues were subjected to gas chromatography-mass spectrometry (GC-MS). A total of seventy-two metabolites were identified and classified into different categories, including carbohydrates, organic acids, amino acids, and alkaloids. Furthermore, RNA-sequencing (RNA-Seq) analysis was performed to explain the molecular mechanism behind it. Thirty-six libraries (twelve samples × three replications) were sequenced, yielding approximately 50 million high-quality clean reads per library. The clean reads of tomato were mapped to tomato (Heinz. cv) reference genome ranging from 91.25% to 95.13%. To investigate the key genes, differentially expressed genes (DEGs) were identified according to the criteria of |log2 (fold change)| ≥1 and a false discovery rate-adjusted p-value (FDR) < 0.05. A total of 2180 genes, of which expression of 553 and 822 were up and down-regulated, respectively, were identified in tomato versus tomato-tomato. However, a total of 3462 genes were differentially expressed, of which expression of 745 and 1096 were up and down-regulated, respectively, in tomato versus tomato-bell. These results indicated that identity recognition causes significant changes in both transcriptomes and metabolomes.

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