Drought is a major abiotic stressor that causes yield losses and limits the growing area for most crops. Soybeans are an important legume crop that is sensitive to water-deficit conditions and suffers heavy yield losses from drought stress. To improve drought-tolerant soybean cultivars through breeding, it is necessary to understand the mechanisms of drought tolerance in soybeans. In this study, we applied several transcriptome datasets obtained from soybean plants under drought stress in comparison to those grown under normal conditions to identify novel drought-responsive genes and their underlying molecular mechanisms. We found 2168 significant up/downregulated differentially expressed genes (DEGs) and 8 core modules using gene co-expression analysis to predict their biological roles in drought tolerance. Gene Ontology and KEGG analyses revealed key biological processes and metabolic pathways involved in drought tolerance, such as photosynthesis, glyceraldehyde-3-phosphate dehydrogenase and cytokinin dehydrogenase activity, and regulation of systemic acquired resistance. Genome-wide analysis of plants’ cis-acting regulatory elements (CREs) and transcription factors (TFs) was performed for all of the identified DEG promoters in soybeans. Furthermore, the PPI network analysis revealed significant hub genes and the main transcription factors regulating the expression of drought-responsive genes in each module. Among the four modules associated with responses to drought stress, the results indicated that GLYMA_04G209700, GLYMA_02G204700, GLYMA_06G030500, GLYMA_01G215400, and GLYMA_09G225400 have high degrees of interconnection and, thus, could be considered as potential candidates for improving drought tolerance in soybeans. Taken together, these findings could lead to a better understanding of the mechanisms underlying drought responses in soybeans, which may useful for engineering drought tolerance in plants.

Oliveria decumbens (Apiaceae) is an aromatic herb traditionally employed in the Persian medicine for the treatment of infectious and gastrointestinal disorders. In the present study, we analyzed the chemical composition of essential oils obtained from different Iranian populations and evaluated their efficacy on a panel of human pathogens (Staphylococcus aureus and Escherichia coli), probiotic (Bacillus subtilis), and phytopathogens (Clavibacter michiganensis, Curtobacterium flaccumfaciens, Xanthomonas citri, and Agrobacterium tumefaciens). The gas chromatographic-mass spectrometry analysis put in evidence four main volatile constituents such as thymol (20.3–36.4%), carvacrol (18.8–33.1%), γ-terpinene (10.6–25.9%), and p-cymene (9.5–17.3%), though with significant variability from an essential oil to another. Notably, the oils from the populations sited in Nourabad Mamasani and Dehdasht showed the highest amount of the phenolic monoterpenes thymol (36.4 and 35.2%, respectively) and carvacrol (33.1 and 30.6%, respectively). The antibacterial activity of O. decumbens essential oils was assessed by the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) methods, showing high activity for the samples from Nourabad Mamasani and Dehdasht populations exhibiting high level of the above phenolics. The obtained MIC and MBC values (mg/ml) were in the ranges 0.0625–2 mg/ml and 1–16 mg/ml, respectively. Noteworthy, in some cases, the antibacterial activity of O. decumbens essential oils was higher than that of chloramphenicol used as positive control. The average MBCs displayed by the O. decumbens samples showed that C. flaccumfaciens had the highest sensitivity to the essential oils. Based on these results, our work shed light on selected O. decumbens populations deserving proper breeding and cultivation strategies in order to warrantee production of bioactive essential oils to be used at pharmaceutical and agricultural level to combat several pathogens.

Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein.

Environmental stresses adversely affect crop growth and yield, resulting in major losses to plants. These stresses occur simultaneously in nature, and we therefore conducted a meta-analysis in this study to identify differential and shared genes, pathways, and transcriptomic mechanisms involved in Arabidopsis response to biotic and abiotic stresses. The results showed a total of 436/21 significant up-/downregulated differentially expressed genes (DEGs) in response to biotic stresses, while 476 and 71 significant DEGs were respectively up- and downregulated in response to abiotic stresses in Arabidopsis thaliana. In addition, 21 DEGs (2.09%) were commonly regulated in response to biotic and abiotic stresses. Except for WRKY45 and ATXTH22, which were respectively up-/down- and down-/upregulated in response to biotic and abiotic stresses, other common DEGs were upregulated in response to all biotic and abiotic treatments. Moreover, the transcription factors (TFs) bHLH, MYB, and WRKY were the common TFs in response to biotic and abiotic stresses. In addition, ath-miR414 and ath-miR5658 were identified to be commonly expressed in response to both biotic and abiotic stresses. The identified common genes and pathways during biotic and abiotic stresses may provide potential candidate targets for the development of stress resistance breeding programs and for the genetic manipulation of crop plants.

Plant viruses participate as biotrophic parasites in complex interactions with their hosts, resulting in the regulation of a diverse range of chloroplast/mitochondria-related genes that are essential for mediating immune responses. In this study, integrative systems biology approaches were applied to identify chloroplast/mitochondrial genes during viral infections caused by a wide number of viruses in Arabidopsis thaliana, tobacco (Nicotiana tabacum L.), and rice (Oryza sativa L.). These findings indicated that 1.5% of the DEGs were common between Arabidopsis/tobacco and Arabidopsis/rice, whereas 0.1% of the DEGs were shared among all species. Approximately 90% of common DEGs are uniquely associated with chloroplasts and mitochondria in the host defense against viral infection and replication. The functions of WRKY, NAC, and MYB transcription factors in imparting resistance to viral infections can be established. Promoter analysis revealed that AP2/EREBP, DOF, and C2H2 zinc finger factors included the most frequent binding sites and played a more important role in plant-viral interactions. Comparative analysis revealed several miRNAs with defensive functions including miRNA156, miRNA160, and miRNA169. The PPI network revealed several key hub genes mostly related to chloroplasts/mitochondria, including ZAT6, CML37, CHLI, DREB, F27B13.20, and ASP2 with upregulation, also PLGG1, PSBY, APO2, POR, ERF, and CSP with downregulation. Moreover, novel hub genes with unknown functions, such as AT2G41640 and AT3G57380 have been identified. This study represents the first preliminary systems biology approach to elucidate the roles of chloroplast/mitochondria-related genes in Arabidopsis, tobacco, and rice against viral challenges by introducing valuable candidate genes for enhanced genetic engineering programs to develop virus-resistant crop varieties.

Fungal infections adversely influence the production and quality of seeds. Previously, Fusarium solani was reported as the causal agent of roselle (Hibiscus sabdariffa L.) seed rot. This study was designed to evaluate the effect of F. solani infection on the germination, biochemical composition, energy reserves, and antioxidant activity of roselle seeds because there is currently a lack of information on the relationship between seed metabolism and infection with F. solani. The results showed that roselle seeds infected with F. solani exhibited a ca. 55% reduction in overall germination. Additionally, the fungal infection decreased antioxidant activity, total phenolic content, protein, sugar (sucrose, fructose, and glucose), and some amino acid (glutamine, serine, and arginine) contents. In contrast, some metabolites were more abundant in infected seeds, including alanine (2.1-fold) and some fatty acids (palmitic acid and heptadecanoic acid by 1.1- and 1.4-fold, respectively). The infection-associated changes in fatty acid profile resulted in the ratio of unsaturated/saturated fatty acids being 2.1-fold higher in infected seeds. Therefore, our results reveal that F. solani infection remarkably altered the biochemical composition of roselle seeds, which may have contributed to the loss of germination and quality of roselle seeds.