The core genes are involved in rice resistance to other pathogens and drought stress
In a larger transcriptome comparison analysis with microarray or RNA-seq datasets deposited in the NCBI GEO database, we investigated the conditions in which the expressions of core genes were regulated. In this analysis, 2308 rice microarray and 355 RNA-seq datasets consisting of various perturbations, such as biotic, abiotic, hormone, nutrient and genetic background alterations, were screened. Consistent with our results, most of the core genes were regulated in the datasets of rice-M. oryzae interactions (Fig. 6A and Supplemental dataset 8). The core genes were also regulated in the rice response to other pathogens, such as the bacteria Xanthomonas oryzae, which causes rice blight disease, and the fungus Ustilaginoidea virens, which causes rice false smut (Fig. 6A, and Supplemental dataset 8). These findings suggested that these genes were common regulators of the rice immune system. Interestingly, more than 80% of the core genes were also regulated under rice drought stress (datasets GSE57950, GSE25176, GSE41647, GSE24048 and GSE92989), indicating the involvement of the core genes in drought stress responses (Fig. 6A and Supplemental dataset 8). Hierarchical clustering of the fold-change of the core genes during different perturbations was conducted to illustrate their regulation patterns (Supplemental dataset 9). The majority of the genes were upregulated in rice infected with M. oryzae, X. oryzae orU. virens , while they were downregulated during drought treatment (Fig. 6B). A similarity comparison showed that the dataset of M. oryzae treatment was similar to the datasets of U. virens andX. oryzae treatments but different from the dataset of drought treatment (Fig. 6C). These analyses indicated that the core genes were involved in both biotic and abiotic stress responses.