Drought stress has a significant impact on photosynthesis in plants, leading to reduced photosynthesis rates and affecting plant growth and yield. Understanding the effects of drought stress on photosynthetic pathways, particularly in C3 and C4 plants, is crucial for maximizing agricultural productivity and maintaining food security. In this study, we analyzed RNA-seq data from leaves of common wheat (Triticum aestivum) and sorghum (Sorghum bicolor), as representatives of C3 and C4, using a meta-analysis approach to investigate the photosynthesis-related genes involved in the response to drought stress. We identified specific genes and components of the photosynthesis pathway that are affected by drought stress. The findings suggest that wheat and sorghum respond differently to drought stress, with sorghum showing a more effective defense system against photoinhibition and damage to photosystems. On the other hand, it seems that in wheat, in order to deal with oxidative stress, the expression of homologous genes of C4 enzyme and genes involved in heme and siroheme synthesis pathway has increased under stress. This is probably due to the higher photoinhibition in C3 photosynthetic system compared to C4. Furthermore, drought stress affected chlorophyll biosynthesis and degradation pathways in both wheat and sorghum, but compared with sorghum, drought stress had a greater inhibitory effect on chlorophyll biosynthesis in wheat, which indicates the difference in their ability to cope with photoinhibition.

The hypericin is assumed as a highly demanded and key bioactive compound, which has antiviral, antimicrobial, antioxidant, and antitumor properties isolated from Hypericum perforatum. Nowadays, increasing bioactive molecules’ contents through generating novel compounds is one of the major research objectives of H. perforatum biotechnology; however, this plant remains recalcitrant and unmanageable to Agrobacterium mediated transformation and genetic improvement programs. In order to overcome these challenges, many researchers have focused on this unruly herb using biotic and abiotic eliciting strategies. Therefore, two experiments were separately designed for the evaluation of two types of abiotic elicitors, aiming at increasing the productivity of hypericin in the adventitious root suspension culture of H. perforatum. The first one was accomplished to evaluate the effect of UV-B light elicitors (the exposure time of 30, 60, and 90 min) and the recovery treatment (with or without) on hypericin content while the second one was assessed the effect of various temperatures (4°C, 8°C, 16°C, and 25°C) in three different exposure times (24 h, 72 h, and 7 d). Based on the results, UV-B (60 min) treatment followed by the recovery produced 0.430 µg/g DW hypericin and was distinguished as the most effective UV-B elicitation treatment. In addition, a temperature of 4°C for a period of 72 hours is required to get the highest amount of hypericin content. These findings indicate the fact that hypericin biosynthesis is notably affected by UV-B exposure time and Low-temperature. The data also clearly elucidate further mechanisms of hypericin production in H. perforatum adventitious root culture.

In Catharanthus roseus, vital plant hormones, namely methyl jasmonate (MeJA) and ethylene, serve as abiotic triggers, playing a crucial role in stimulating the production of specific secondary compounds with anticancer properties. Understanding how plants react to various stresses, stimuli, and the pathways involved in biosynthesis holds significant promise. The application of stressors like ethylene and MeJA induces the plant's defense mechanisms, leading to increased secondary metabolite production. To delve into the essential transcriptomic processes linked to hormonal responses, this study employed an integrated approach combining RNA-Seq data meta-analysis and system biology methodologies. Furthermore, the validity of the meta-analysis findings was confirmed using RT-qPCR. Within the meta-analysis, 903 genes exhibited differential expression (DEGs) when comparing normal conditions to those of the treatment. Subsequent analysis, encompassing gene ontology, KEGG, TF, and motifs, revealed that these DEGs were actively engaged in multiple biological processes, particularly in responding to various stresses and stimuli. Additionally, these genes were notably enriched in diverse biosynthetic pathways, including those related to TIAs, housing valuable medicinal compounds found in this plant. Furthermore, by conducting co-expression network analysis, we identified hub genes within modules associated with stress response and the production of TIAs. Most genes linked to the biosynthesis pathway of TIAs clustered within three specific modules. Noteworthy hub genes, including Helicase ATP-binding domain, hbdA, and ALP1 genes within the blue, turquoise, and green module networks, are presumed to play a role in the TIAs pathway. These identified candidate genes hold potential for forthcoming genetic and metabolic engineering initiatives aimed at augmenting the production of secondary metabolites and medicinal compounds within C. roseus.

The current bioinformatics study was undertaken to analyze the transcriptome of chicken (Gallus gallus) after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually. Different undirected networks were constructed and their metrics determined e.g., degree centrality, closeness centrality, harmonic centrality, subgraph centrality and eigenvector centrality. The results showed that, based on criteria of centrality, the CMTR1, EPSTI1, RNF213, HERC4L, IFIT5 and LY96 genes were the most significant during HPAI challenge, with PARD6G, HMG20A, PEX14, RNF151 and TLK1L having the lowest values. However, for LPAI challenge, ZDHHC9, IMMP2L, COX7C, RBM18, DCTN3, and NDUFB1 genes had the largest values for aforementioned criteria, with GTF3C5, DROSHA, ATRX, RFWD2, MED23 and SEC23B genes having the lowest values. The results of this study can be used as a basis for future development of treatments/preventions of the effects of avian influenza in chicken.

Wheat is the most important cereal. One of the environmental stresses is drought that harm the production of many cereals and every year due to low rainfall and frequent droughts, the need to produce plants resistant to this stress is felt. Therefore, identification and evaluation of the genes involved in the production of this resistance in plants are of great importance. By identifying these genes and changing their expression, it is possible to produce resistant plants that can tolerate dehydration and drought, with at least a qualitative and quantitative reduction in yield. Based on the meta-analysis results obtained in this study, in resistant cultivars ~ 4% (2394/61290) of the probe IDs decreased and ~ 4.5% (2670/61290) increased expression, furthermore in susceptible cultivars ~ 7% (4183/61290) of probe IDs decreased and ~ 6% (3591/61290) increased expression (P value ≤ 0.05). List of up- and downregulated genes was revealed, among the expressed genes of transcription factors Myb3, ethylene-responsive 5a, MIKC-type MADS-box WM24B, and salinity inducible ERF4 in resistant cultivars and transcription factors WRKY15, MADS-box TaAGL8, WRKY39, and Myb in susceptible cultivars, they showed a significant increase in expression, these transcription factors are of great importance in drought stress. Among them, ethylene responsive 5a in resistant cultivars by 3 times and Myb in susceptible cultivars by 2.6 times have shown the highest expression change. Using Cytoscape Hub software, the Phosphoenolpyruvate carboxylase (PEPC) and lyase isocitrate (TaSAG7) genes, which have significantly different expressions in resistant and susceptible wheat cultivars. PEPC and TaSAG7 genes were upregulated in resistant wheat cultivars as well as down regulated in susceptible cultivars. Also, the qPCR results of selected genes were consistent with the outcomes of the meta-analysis. All microarray data were collected from the NCBI Gene Expression Omnibus site. Libraries with drought-tolerant and susceptible cultivars for wheat were considered under the stress and control conditions from whole leaf tissue. By meta-analysis combined the purposeful results of multiple experiments, and found list of genes expressed in reverse between the two cultivars. These genes can distinguish between different susceptible and resistant wheat cultivars.