The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence

Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales–other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.publishedVersio

Genome-wide annotation and expression analysis of WRKY and bHLH transcriptional factor families reveal their involvement under cadmium stress in tomato (Solanum lycopersicum L.)

The WRKY and bHLH transcription factors have been implicated in the regulation of gene expression during various physiological processes in plants, especially in plant stress responses. However, little information about the heavy metal-responsive SlWRKY and SlbHLH in tomato (Solanum lycopersicum) is available. We performed a genome-wide investigation for these two TF families in S. lycopersicum and determined their role in cadmium (Cd) stress tolerance. Furthermore, ortholog analysis with the Arabidopsis genome led to classifying WRKY and bHLH ortholog genes into nine and 11 clusters, respectively. The comparative phylogenetic analysis revealed duplication events and gene loss in Arabidopsis and S. lycopersicum, which occurred during evolution both before and after the last common ancestor of the two species. Orthologous relationships are also supported by additional evidence, such as gene structure, conserved motif compositions, and protein–protein interaction networks for the majority of genes, suggesting their similar functions. A comprehensive transcriptomics analysis revealed that both WRKY and bHLH genes were differentially expressed in response to cadmium stress as compared with control plants. A gene ontology analysis revealed that most WRKYs and bHLHs are DNA-binding essential proteins that regulate gene expression positively and negatively. Analyses of interaction networks revealed that both WRKYs and bHLHs mediate networks implicated in several stress-signaling pathways. The findings of this work may help us to comprehend the intricate transcriptional control of WRKY and bHLH genes and identify potential stress-responsive genes relevant to tomato genetic improvement. Moreover, identifying heavy metal stress-responsive WRKY and bHLH genes in S. lycopersicum will provide fundamental insights for developing new heavy metal stress-tolerant varieties of tomato crops

Dynamic interplay of WRKY, GRAS, and ERF transcription factor families in tomato-endophytic fungal symbiosis: insights from transcriptome and genome-wide analysis

Plant-microbe interactions play a crucial role in shaping plant growth and development, as well as in mediating plant responses to biotic and abiotic stresses. In this study, we used RNA-seq data to examine the expression profiles of SlWRKY, SlGRAS, and SlERF genes during the symbiotic association of Curvularia lunata SL1 with tomato (Solanum lycopersicum) plants. We also conducted functional annotation analysis by comparative genomics studies of their paralogs and orthologs genes, as well as other approaches, such as gene analysis and protein interaction networks, to identify and characterize the regulatory roles of these TFs in the development of the symbiotic association. We found that more than half of the investigated SlWRKY genes exhibited significant upregulation during symbiotic association, including SlWRKY38, SlWRKY46, SlWRKY19, and SlWRKY51. Several SlGRAS and SlERF genes were upregulated, such as SlGLD2, SlGLD1, SlERF.C.5, ERF16, and SlERF.B12. Conversely, a smaller proportion of SlWRKY, SlGRAS, and SlERF genes were significantly downregulated during symbiotic association. Furthermore, we investigated the possible roles of SlWRKY, SlGRAS, and SlERF genes in hormonal regulation during plant-microbe interactions. We identified several upregulated candidate transcripts likely to be involved in plant hormone signaling pathways. Our findings are consistent with previous studies on these genes, providing further evidence of their involvement in hormonal regulation during plant-microbe interactions. To validate the RNA-seq data accuracy, we performed RT-qPCR analyses of selected SlWRKY, SlGRAS, and SlERF genes, which showed similar expression patterns to those observed in the RNA-seq data. These results confirmed the accuracy of our RNA-seq data and provided additional support for the differential expression of these genes during plant-microbe interactions. Taken together, our study provides new insights into the differential expression profiles of SlWRKY, SlGRAS, and SlERF genes during symbiotic association with C. lunata, as well as their potential roles in hormonal regulation during plant-microbe interactions. These findings could be useful for guiding future research on the ways in which plants and microbes interact, and may ultimately lead to the creation of better approaches for promoting plant growth under stressful conditions

Exploring the potential of halotolerant bacteria from coastal regions to mitigate salinity stress in wheat: physiological, molecular, and biochemical insights

Salinity stress, a significant global abiotic stress, is caused by various factors such as irrigation with saline water, fertilizer overuse, and drought conditions, resulting in reduced agricultural production and sustainability. In this study, we investigated the use of halotolerant bacteria from coastal regions characterized by high salinity as a solution to address the major environmental challenge of salinity stress. To identify effective microbial strains, we isolated and characterized 81 halophilic bacteria from various sources, such as plants, rhizosphere, algae, lichen, sea sediments, and sea water. We screened these bacterial strains for their plant growth-promoting activities, such as indole acetic acid (IAA), phosphate solubilization, and siderophore production. Similarly, the evaluation of bacterial isolates through bioassay revealed that approximately 22% of the endophytic isolates and 14% of rhizospheric isolates exhibited a favorable influence on seed germination and seedling growth. Among the tested isolates, GREB3, GRRB3, and SPSB2 displayed a significant improvement in all growth parameters compared to the control. As a result, these three isolates were utilized to evaluate their efficacy in alleviating the negative impacts of salt stress (150 mM, 300 mM, and seawater (SW)) on the growth of wheat plants. The result showed that shoot length significantly increased in plants inoculated with bacterial isolates up to 15% (GREB3), 16% (GRRB3), and 24% (SPSB2), respectively, compared to the control. The SPSB2 strain was particularly effective in promoting plant growth and alleviating salt stress. All the isolates exhibited a more promotory effect on root length than shoot length. Under salt stress conditions, the GRRB3 strain significantly impacted root length, leading to a boost of up to 6%, 5%, and 3.8% at 150 mM, 300 mM, and seawater stress levels, respectively. The bacterial isolates also positively impacted the plant’s secondary metabolites and antioxidant enzymes. The study also identified the WDREB2 gene as highly upregulated under salt stress, whereas DREB6 was downregulated. These findings demonstrate the potential of beneficial microbes as a sustainable approach to mitigate salinity stress in agriculture

Global disparities in surgeons’ workloads, academic engagement and rest periods: the on-calL shIft fOr geNEral SurgeonS (LIONESS) study

: The workload of general surgeons is multifaceted, encompassing not only surgical procedures but also a myriad of other responsibilities. From April to May 2023, we conducted a CHERRIES-compliant internet-based survey analyzing clinical practice, academic engagement, and post-on-call rest. The questionnaire featured six sections with 35 questions. Statistical analysis used Chi-square tests, ANOVA, and logistic regression (SPSS® v. 28). The survey received a total of 1.046 responses (65.4%). Over 78.0% of responders came from Europe, 65.1% came from a general surgery unit; 92.8% of European and 87.5% of North American respondents were involved in research, compared to 71.7% in Africa. Europe led in publishing research studies (6.6 ± 8.6 yearly). Teaching involvement was high in North America (100%) and Africa (91.7%). Surgeons reported an average of 6.7 ± 4.9 on-call shifts per month, with European and North American surgeons experiencing 6.5 ± 4.9 and 7.8 ± 4.1 on-calls monthly, respectively. African surgeons had the highest on-call frequency (8.7 ± 6.1). Post-on-call, only 35.1% of respondents received a day off. Europeans were most likely (40%) to have a day off, while African surgeons were least likely (6.7%). On the adjusted multivariable analysis HDI (Human Development Index) (aOR 1.993) hospital capacity > 400 beds (aOR 2.423), working in a specialty surgery unit (aOR 2.087), and making the on-call in-house (aOR 5.446), significantly predicted the likelihood of having a day off after an on-call shift. Our study revealed critical insights into the disparities in workload, access to research, and professional opportunities for surgeons across different continents, underscored by the HDI

Over-Expression of Chorismate Mutase Enhances the Accumulation of Salicylic Acid, Lignin, and Antioxidants in Response to the White-Backed Planthopper in Rice Plants

The white-backed planthopper (WBPH) is a serious pest of rice crop and causes sever yield loss each year, especially in Asian countries. In this study, we used chorismate mutase (CM) transgenic line to examine the defense mechanism of rice plants against WBPH. The survival rate of WBPHs, infestation rate of plants, lignin biosynthesis, transcriptional regulation of related genes, salicylic acid (SA) accumulation and signaling and antioxidants regulation were investigated. The WBPH population decreased by 67% in OxCM-t, and the plant infestation rate was 3.5-fold higher in wild-type plants compared with transgenic plants. A substantial increase in lignin was found in the transgenic line (742%) and wild-type (417%) plants. Additionally, CM, phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and chalcone isomerase (CHI) showed significant increases in their relative expression level in the transgenic line. Salicylic acid was significantly enhanced in the transgenic line compared with WBPH infestation. SA can activate pathogenesis related proteins-1 (PR1), PR2, antioxidants, and the expression of their related genes: superoxide dismutase (SOD) and catalase (CAT). WBPH infestation reduced the chlorophyll contents of both transgenic and wild-type plants, but the reduction was great in wild-type than transgenic plants. The sugar content was only significantly increased in the transgenic line, indicating that sugars are not heavily involved in WBPH stress. Phenylalanine, proline, aspartic acid, and total amino acids were increased in the transgenic line and reduced in the wild-type plants. Taken together, all the results suggest that overexpression of CM gene regulates the defense mechanisms and enhances the rice toward WBPH stress

Metal Resistant Endophytic Bacteria Reduces Cadmium, Nickel Toxicity, and Enhances Expression of Metal Stress Related Genes with Improved Growth of Oryza Sativa, via Regulating Its Antioxidant Machinery and Endogenous Hormones

The tolerance of plant growth-promoting endophytes (PGPEs) against various concentrations of cadmium (Cd) and nickel (Ni) was investigated. Two glutathione-producing bacterial strains (Enterobacter ludwigii SAK5 and Exiguobacterium indicum SA22) were screened for Cd and Ni accumulation and tolerance in contaminated media, which showed resistance up to 1.0 mM. Both strains were further evaluated by inoculating specific plants with the bacteria for five days prior to heavy metal treatment (0.5 and 1.0 mM). The enhancement of biomass and growth attributes such as the root length, shoot length, root fresh weight, shoot fresh weight, and chlorophyll content were compared between treated inoculated plants and treated non-inoculated plants. Both strains significantly increased the accumulation of Cd and Ni in inoculated plants. The accumulation of both heavy metals was higher in the roots than in the shoots, however; Ni accumulation was greater than Cd. Heavy metal stress-responsive genes such as OsGST, OsMTP1, and OsPCS1 were significantly upregulated in treated non-inoculated plants compared with treated inoculated plants, suggesting that both strains reduced heavy metal stress. Similarly, abscisic acid (ABA) was increased with increased heavy metal concentration; however, it was reduced in inoculated plants compared with non-inoculated plants. Salicylic acid (SA) was found to exert synergistic effects with ABA. The application of suitable endophytic bacteria can protect against heavy metal hyperaccumulation by enhancing detoxification mechanisms

Discovery and Validation of a Novel Step Catalyzed by OsF3H in the Flavonoid Biosynthesis Pathway

Kaempferol and quercetin are the essential plant secondary metabolites that confer huge biological functions in the plant defense system. In this study, biosynthetic pathways for kaempferol and quercetin were constructed in Saccharomyces cerevisiae using naringenin as a substrate. OsF3H was cloned into pRS42K yeast episomal plasmid (YEp) vector and the activity of the target gene was analyzed in engineered and empty strains. We confirmed a novel step of kaempferol and quercetin biosynthesis directly from naringenin, catalyzed by the rice flavanone 3-hydroxylase (F3H). The results were confirmed through thin layer chromatography (TLC) followed by western blotting, nuclear magnetic resonance (NMR), and liquid chromatography-mass spectrometry LCMS-MS. TLC showed positive results when comparing both compounds extracted from the engineered strain with the standard reference. Western blotting confirmed the lack of OsF3H activity in empty strains and confirmed high OsF3H expression in engineered strains. NMR spectroscopy confirmed only quercetin, while LCMS-MS results revealed that F3H is responsible for the conversion of naringenin to both kaempferol and quercetin

Bioactivity and Therapeutic Potential of Kaempferol and Quercetin: New Insights for Plant and Human Health

Plant secondary metabolites, especially flavonoids, are major metabolites widely found in plants that play several key roles in plant defence and signalling in response to stress conditions. The most studied among these flavonoids are kaempferol and quercetin due to their anti-oxidative potential and their key roles in the defence system, making them more critical for plant adaptation in stress environments. Kaempferol and quercetin in plants have great therapeutic potential for human health. Despite being well-studied, some of their functional aspects regarding plants and human health need further evaluation. This review summarizes the emerging potential of kaempferol and quercetin in terms of antimicrobial activity, bioavailability and bioactivity in the human body as well as in the regulation of plant defence in response to stresses and as a signalling molecule in terms of hormonal modulation under stress conditions. We also evaluated the safe use of both metabolites in the pharmaceutical industry

Exogenous Phytohormones and Fertilizers Enhance Jatropha curcas L. Growth through the Regulation of Physiological, Morphological, and Biochemical Parameters

Jatropha curcas L. is a perennial plant, that emerged as a biodiesel crop attracting the great interest of researchers. However, it is considered a semi-wild plant and needed to apply crop-improving practices to enhance its full yield potential. This study was conducted to improve the growth and development of the J. curcas plant by exogenous application of Gibberellic acid (GA), indole acetic acid (IAA), and fertilizer (nitrogen, phosphorus, potassium (NPK)). The experiment was conducted in pots in triplicate and 100 ppm and 250 ppm of GA and IAA were applied separately while NPK was applied in two levels (30 and 60 g/pot). The results revealed a significant difference in growth parameters with the application of hormones and fertilizer. The highest shoot length (47%), root length (63%), root fresh weight (72%), and root dry weight (172%) were shown by plants treated with GA 250 ppm. While plants treated with NPK 60 g showed the highest increases in shoot fresh weight and shoot dry weight compared to control plants. The highest increase in leaves number (274%) and branches number (266%) were shown by the plants treated with GA 100 ppm and GA 250 ppm, respectively, while GA 250 ppm and IAA 250 ppm highly increased stem diameter (123%) and stem diameter was also shown by GA 250 ppm-treated plants. NPK 60 g highly increased proximate composition (protein content, carbohydrate, fat, moisture content, and ash content) compare with hormones and control plants. Our results concluded the optimized concentration of IAA, GA, and NPK significantly increases J. curcas growth vigor