Comprehensive transcriptomic meta-analysis unveils new responsive genes to methyl jasmonate and ethylene in Catharanthusroseus.

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.

A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress.

The main factor leading to a decrease in crop productivity is abiotic stresses, particularly drought. Plants with C4 and CAM photosynthesis are better adapted to drought-prone areas than C3 plants. Therefore, it is beneficial to compare the stress response of plants with different photosynthetic pathways. Since most crops are C3 and C4 plants, this study focused on conducting an RNA-seq meta-analysis to investigate and compare how C3 and C4 plants respond to drought stress at the gene expression level in their leaves. Additionally, the accuracy of the meta-analysis results was confirmed with RT-qPCR. Based on the functional enrichment and network analysis, hub genes related to ribosomal proteins and photosynthesis were found to play a potential role in stress response. Moreover, our findings suggest that the low abundant amino acid degradation pathway, possibly through providing ATP source for the TCA cycle, in both groups of plants and the activation of the OPPP pathway in C4 plants, through providing the electron source required by this plant, can help to improve drought stress tolerance.

Meta-analysis highlights the key drought responsive genes in genes: PEPC and TaSAG7 are hubs response networks.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

"Is Omicron mild"? Testing this narrative with the mutational landscape of its three lineages and response to existing vaccines and therapeutic antibodies.

SARS-CoV-2 Omicron with its lineages BA.1, BA.2, and BA.3 has triggered a fresh wave of Covid-19 infections. Though, Omicron has, so far, produced mild symptoms, its genome contains 60 mutations including 37 in the spike protein and 15 in the receptor-binding domain. Thirteen sites conserved in previous SARS-CoV-2 variants carry mutations in Omicron. Many mutations have shown evolution under positive selection. Omicron's giant mutational leap has raised concerns as there are signs of higher virus infectivity rate, pathogenesis, reinfection, and immune evasion. Preliminary studies have reported waning of immunity after two-dose primary vaccine regime, need for the boosters, folds reduction in vaccine effectiveness and neutralizing antibodies even after boosting and significant neutralization resistance with the therapeutic monoclonal, polyclonal, and convalescent antibodies against Omicron. The narrative that "Omicron is mild," therefore, needs time to be tested with a deeper, scientific dwelling into the facts.

Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing.

BACKGROUND: Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. METHODS AND RESULTS: Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. CONCLUSIONS: The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.

Identification and verification of seed development related miRNAs in kernel almond by small RNA sequencing and qPCR.

Many studies have investigated the role of miRNAs on the yield of various plants, but so far, no report is available on the identification and role of miRNAs in fruit and seed development of almonds. In this study, preliminary analysis by high-throughput sequencing of short RNAs of kernels from the crosses between almond cultivars 'Sefid' × 'Mamaee' (with small and large kernels, respectively) and 'Sefid' × 'P. orientalis' (with small kernels) showed that the expressions of several miRNAs such as Pdu-miR395a-3p, Pdu-miR8123-5p, Pdu-miR482f, Pdu-miR6285, and Pdu-miR396a were significantly different. These miRNAs targeted genes encoding different proteins such as NYFB-3, SPX1, PGSIP3 (GUX2), GH3.9, and BEN1. The result of RT-qPCR revealed that the expression of these genes showed significant differences between the crosses and developmental stages of the seeds, suggesting that these genes might be involved in controlling kernel size because the presence of these miRNAs had a negative effect on their target genes. Pollen source can influence kernel size by affecting hormonal signaling and metabolic pathways through related miRNAs, a phenomenon known as xenia.

Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics.

Crown imperial (CI) has been used in traditional medicine. Today it is known that such beneficial effects are due to its richness in steroidal alkaloids (SA). Using de novo transcriptomics, orthologues/paralogues finder, phylogenetic analysis and tissue- and developmental stage-specific expression analysis, we identified ten genes and several TFs involved in the biosynthesis of SA in CI. The comparative analysis of ten genes expression profiles revealed the possibility of their co-regulation, which may imply the possibility of their organization in metabolic gene clusters. Having in mind convergent evolution of steroidal biosynthetic pathways in flowering plants and records of convergent evolution of specific proteins, observed expression patterns open a reasonable interest to investigate the possibility of the existence of genes cluster organization in SA pathway in the family Liliaceae or at least in some species of genus Fritillaria. Obtained results support transcriptomics as useful approach in elucidating genes underlying complex biochemical pathways.

In silico search and biological validation of microRNAs related to drought response in peach and almond.

Plant responses to drought stress are regulated at the transcriptional and post-transcriptional levels through noncoding endogenous microRNAs. These microRNAs play key roles in gene expression, mainly by down-regulating target mRNAs. In this work, an in silico search and validation for microRNAs related to drought response in peach ('G.H. Hill'), almond ('Sefied') and an interspecific peach-almond hybrid ('GN 15') has been performed. We used qPCR to analyse the gene expression of several miRNAs described as being related to drought response in peach, including miR156, miR159, miR160, miR167, miR171, miR172, miR398, miR403, miR408, miR842 and miR2275 under mild and severe water deficit. These miRNAs were in silico selected on the basis of previous works, their conservation in plants and their drought response. qPCR analysis confirmed the implication of these miRNAs in the dehydration stress response in the three assayed genotypes. Comparison of miRNA expression patterns in the three evaluated genotypes indicated that the hybrid GN 15 showed higher expression levels of specific miRNAs which should be related to the observed drought tolerance. mRNA target transcripts of the miRNAs studied were predicted using the Rose database, which includes transcription factors that regulate plant growth and development. In addition, results showed that the promoter region contains responsive elements to hormone-mediated regulatory elements. Network analysis not only unravelled the interaction between miRNAs and their predicted gene targets but also highlighted the roles of miRNAs in response to drought stress.

The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress.

Spring frost is an important environmental stress that threatens the production of Prunus trees. However, little information is available regarding molecular response of these plants to the frost stress. Using high throughput sequencing, this study was conducted to identify differentially expressed miRNAs, both the conserved and the non-conserved ones, in the reproductive tissues of almond tolerant H genotype under cold stress. Analysis of 50 to 58 million raw reads led to identification of 174 unique conserved and 59 novel microRNAs (miRNAs). Differential expression pattern analysis showed that 50 miRNA families were expressed differentially in one or both of almond reproductive tissues (anther and ovary). Out of these 50 miRNA families, 12 and 15 displayed up-regulation and down-regulation, respectively. The distribution of conserved miRNA families indicated that miR482f harbor the highest number of members. Confirmation of miRNAs expression patterns by quantitative real- time PCR (qPCR) was performed in cold tolerant (H genotype) alongside a sensitive variety (Sh12 genotype). Our analysis revealed differential expression for 9 miRNAs in anther and 3 miRNAs in ovary between these two varieties. Target prediction of miRNAs followed by differential expression analysis resulted in identification of 83 target genes, mostly transcription factors. This study comprehensively catalogued expressed miRNAs under different temperatures in two reproductive tissues (anther and ovary). Results of current study and the previous RNA-seq study, which was conducted in the same tissues by our group, provide a unique opportunity to understand the molecular basis of responses of almond to cold stress. The results can also enhance the possibility for gene manipulation to develop cold tolerant plants.

Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus.

Biotic and abiotic stresses affect plant development and production through alternation of the gene expression pattern. Gene expression itself is under the control of different regulators such as miRNAs and transcription factors (TFs). MiRNAs are known to play important roles in regulation of stress responses via interacting with their target mRNAs. Here, for the first time, seven conserved miRNAs, associated with drought, heat, salt and cadmium stresses were characterized in sunflower. The expression profiles of miRNAs and their targets were comparatively analyzed between leaves and roots of plants grown under the mentioned stress conditions. Gene ontology analysis of target genes revealed that they are involved in several important pathways such as auxin and ethylene signaling, RNA mediated silencing and DNA methylation processes. Gene regulatory network highlighted the existence of cross-talks between these stress-responsive miRNAs and the other stress responsive genes in sunflower. Based on network analysis, we suggest that some of these miRNAs in sunflower such as miR172 and miR403 may play critical roles in epigenetic responses to stress. It seems that depending on the stress type, theses miRNAs target several pathways and cellular processes to help sunflower to cope with drought, heat, salt and cadmium stress conditions in a tissue-associated manner.

RNA-seq SSRs and small RNA-seq SSRs: new approaches in cancer biomarker discovery.

The recent exponential increase in the number of next generation sequencing studies provides a new source of data for the discovery of functional genomics based markers. The RNA-seq and small RNA-seq provide a new source for the discovery of differentially expressed SSRs (simple sequence repeats) as biomarkers in various diseases. In the present study, for the first time, we applied RNA-seq SSR to find new biomarkers for pancreatic cancer (PC) diagnosis. Analysis of RNA-seq data revealed a significant alternation in the frequency of SSR motifs during cancer progression. In particular, RNA-seq SSR showed an increase in the frequencies of GCC/GGC and GCG/CGC motifs in PC samples compared to healthy pancreas. These findings were further confirmed using meta-analysis of EST-SSR data in 11 different cancers. Interestingly, the genes containing GCC/GGC and GCG/CGC motifs in their sequences were involved in many cancer-related biological processes, particularly regulation processes. The small RNA-seq data were also mined for the conserved patterns in SSR frequencies (sRNA-seq SSR) during cancer progression. Based on the results, we suggest the potential use of GCC/GGC and GCG/CGC motifs as biomarkers in PC. Based on the findings of this study, it seems that RNA-seq SSR and sRNA-seq SSR could open a new paradigm in the diagnostic and even therapeutic strategies for PC along the other types of cancers.

De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress.

Almond (Prunus dulcis Mill.), one of the most important nut crops, requires chilling during winter to develop fruiting buds. However, early spring chilling and late spring frost may damage the reproductive tissues leading to reduction in the rate of productivity. Despite the importance of transcriptional changes and regulation, little is known about the almond's transcriptome under the cold stress conditions. In the current research, we used RNA-seq technique to study the response of the reproductive tissues of almond (anther and ovary) to frost stress. RNA sequencing resulted in more than 20 million reads from anther and ovary tissues of almond, individually. About 40,000 contigs were assembled and annotated de novo in each tissue. Profile of gene expression in ovary showed significant alterations in 5,112 genes, whereas in anther 6,926 genes were affected by freezing stress. Around two thousands of these genes were common altered genes in both ovary and anther libraries. Gene ontology indicated the involvement of differentially expressed (DE) genes, responding to freezing stress, in metabolic and cellular processes. qRT-PCR analysis verified the expression pattern of eight genes randomly selected from the DE genes. In conclusion, the almond gene index assembled in this study and the reported DE genes can provide great insights on responses of almond and other Prunus species to abiotic stresses. The obtained results from current research would add to the limited available information on almond and Rosaceae. Besides, the findings would be very useful for comparative studies as the number of DE genes reported here is much higher than that of any previous reports in this plant.

Molecular Survey of Toxoplasma gondii in Sheep, Cattle and Meat Products in Chaharmahal va Bakhtiari Province, Southwest of Iran.

BACKGROUND: Toxoplasmosis is a worldwide spread disease. The present study examined the prevalence of Toxoplasma gondii infection among animals of edible meat (cattle and sheep) in Chaharmahal va Bakhtiari Province (Southwest of Iran) in 2012. Furthermore, we attempted for the first time to identify this parasite from the meat products in the province. METHODS: The tongue, brain, femur muscle and liver of 50 sheep and 70 cattle as well as 50 samples of meat products were selected and collected to perform molecular survey using Nested-PCR method. RESULTS: Of the studied sheep, 38% were infected. The infection rate in the age groups under 1 year, 1-2 years, and more than 2 years was 25%, 35.29% and 52.94%, respectively. The infection rate in femur muscle, brain, liver and tongue was 28%, 32%, 30% and 16%, respectively. Of the studied cattle, 8.57% were infected. The infection rate in the age groups 1-2 years, 2-4 years, and more than 4 years was 3.7%, 9.09% and 14.28%, respectively. Sheep was infected 6 times more than cattle (OR = 6.53 CI = 2.374-18.005).The infection rate among samples of meat products was 12% (6 samples out of 50 samples). CONCLUSION: Due to the high rate of this parasitic infection among the slaughtered animals as well as meat products in this region, the use of infected material can be one of the main risk factors of transmission of the parasite to humans.

Control of abscisic acid catabolism and abscisic acid homeostasis is important for reproductive stage stress tolerance in cereals.

Drought stress at the reproductive stage causes pollen sterility and grain loss in wheat (Triticum aestivum). Drought stress induces abscisic acid (ABA) biosynthesis genes in anthers and ABA accumulation in spikes of drought-sensitive wheat varieties. In contrast, drought-tolerant wheat accumulates lower ABA levels, which correlates with lower ABA biosynthesis and higher ABA catabolic gene expression (ABA 8'-hydroxylase). Wheat TaABA8'OH1 deletion lines accumulate higher spike ABA levels and are more drought sensitive. ABA treatment of the spike mimics the effect of drought, causing high levels of sterility. ABA treatment represses the anther cell wall invertase gene TaIVR1, and drought-tolerant lines appeared to be more sensitive to the effect of ABA. Drought-induced sterility shows similarity to cold-induced sterility in rice (Oryza sativa). In cold-stressed rice, the rate of ABA accumulation was similar in cold-sensitive and cold-tolerant lines during the first 8 h of cold treatment, but in the tolerant line, ABA catabolism reduced ABA levels between 8 and 16 h of cold treatment. The ABA biosynthesis gene encoding 9-cis-epoxycarotenoid dioxygenase in anthers is mainly expressed in parenchyma cells surrounding the vascular bundle of the anther. Transgenic rice lines expressing the wheat TaABA8'OH1 gene under the control of the OsG6B tapetum-specific promoter resulted in reduced anther ABA levels under cold conditions. The transgenic lines showed that anther sink strength (OsINV4) was maintained under cold conditions and that this correlated with improved cold stress tolerance. Our data indicate that ABA and ABA 8'-hydroxylase play an important role in controlling anther ABA homeostasis and reproductive stage abiotic stress tolerance in cereals.

Importance of pre-anthesis anther sink strength for maintenance of grain number during reproductive stage water stress in wheat.

Reproductive stage water stress leads to spikelet sterility in wheat. Whereas drought stress at anthesis affects mainly grain size, stress at the young microspore stage of pollen development is characterized by abortion of pollen development and reduction in grain number. We identified genetic variability for drought tolerance at the reproductive stage. Drought-tolerant wheat germplasm is able to maintain carbohydrate accumulation in the reproductive organs throughout the stress treatment. Starch depletion in the ovary of drought-sensitive wheat is reversible upon re-watering and cross-pollination experiments indicate that the ovary is more resilient than the anther. The effect on anthers and pollen fertility is irreversible, suggesting that pollen sterility is the main cause of grain loss during drought conditions in wheat. The difference in storage carbohydrate accumulation in drought-sensitive and drought-tolerant wheat is correlated with differences in sugar profiles, cell wall invertase gene expression and expression of fructan biosynthesis genes in anther and ovary (sucrose : sucrose 1-fructosyl-transferase, 1-SST; sucrose : fructan 6-fructosyl-transferase, 6-SFT). Our results indicate that the ability to control and maintain sink strength and carbohydrate supply to anthers may be the key to maintaining pollen fertility and grain number in wheat and this mechanism may also provide protection against other abiotic stresses.