Bioscience Methods 2024, Vol.15, No.3, 102-113 http://bioscipublisher.com/index.php/bm 105 Studies employing advanced transcriptomic techniques such as RNA sequencing (RNA-seq) were selected to ensure high-quality and comprehensive data. The use of microdissection-based RNA sequencing in (Jeon et al., 2020) exemplifies the application of advanced techniques to obtain high-quality transcriptomes of both the pathogen and the host during infection. To cover a broad spectrum of rice-pathogen interactions, studies involving different pathogens and various resistance mechanisms were included. For example, the study by (Zhang et al., 2020) on the response of rice to Rice black-streaked dwarf virus (RBSDV) infection provided insights into the regulatory networks involving long non-coding RNAs (lncRNAs) and mRNAs, highlighting the diversity of pathogen interactions and defense responses. Studies that integrated genomic and genetic analyses to identify resistance loci and gene interactions were also considered. The research by (Wisser et al., 2005) on the identification and characterization of regions of the rice genome associated with broad-spectrum, quantitative disease resistance is a prime example of such an approach, providing a framework for understanding the genetic basis of disease resistance. Preference was given to studies that reported novel findings or made significant contributions to the field of plant-pathogen interactions. The discovery of a new pathogen effector and its interaction with rice immune receptors in Sugihara et al., (2022) illustrates the type of groundbreaking research that was prioritized. 4.2 Detailed analysis of a specific rice-pathogen interaction using transcriptomics In the study of rice-pathogen interactions, transcriptomic approaches have provided significant insights into the molecular dynamics between rice and its pathogens. One notable example is the interaction between rice and the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial leaf blight, a devastating disease affecting rice crops globally. A detailed transcriptomic analysis was conducted to understand the interaction between rice and Xoo, focusing on the roles of host-induced carbohydrate metabolism enzymes in Xoo virulence and the rice defense response. Using comparative proteomics and transcriptomics, researchers identified two novel host-induced virulence factors, XanA and Imp, in Xoo. These factors were shown to significantly affect the global gene expression profiles in susceptible rice varieties (Wu et al., 2021). The study revealed that mutants of the carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses in rice and nearly abolished Xoo virulence. Transcriptomic analysis of rice treated with these mutants identified a total of 1 521 and 227 differentially expressed genes (DEGs) for PXO99A vs Δimp at 1 and 3 days post-inoculation (dpi), respectively, and 131 and 106 DEGs for PXO99A vs ΔxanA at the same time points. These DEGs were involved in various biological processes, including photosynthesis, signal transduction, oxidation-reduction, and the metabolism of carbohydrates, lipids, amino acids, secondary metabolites, and hormones (Wu et al., 2021). Further analysis using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and MapMan revealed that while many pathways were associated with both Δimp and ΔxanA treatments, the underlying genes were not the same. This indicates that although the overall defense mechanisms might be similar, the specific genes involved in these processes differ depending on the virulence factor (Figure 1) (Wu et al., 2021). Another study employing dual RNA-seq provided additional insights into the rice-Xoo interaction. This approach allowed simultaneous examination of the transcriptomes of both rice and Xoo during infection. The study found that the type three secretion system (T3SS) of Xoo plays a crucial role in its pathogenic lifestyle. In rice inoculated with a T3SS-defective strain, significant changes were observed in the expression of plant defense-related genes, including those involved in plant signaling pathways and the biosynthesis of phenylalanine, flavonoids, and momilactones. These changes suggest a repression of plant defense responses and a reduction in callose deposition and phytoalexin accumulation, which are critical for plant immunity (Liao et al., 2019). 4.3 Interpretation of key findings from the case study The transcriptomic approaches to studying rice-pathogen interactions have yielded significant insights into the molecular mechanisms underlying these complex biological processes. One of the key findings from the case study on the rice blast fungus Magnaporthe oryzae and its host Oryza sativa is the high-quality transcriptome data obtained using a microdissection-based RNA sequencing approach. This method allowed for a comprehensive expression profiling of both the fungal pathogen and the rice host during infection, providing a valuable resource
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