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<jats:p>Chromium (Cr) is a toxic heavy metal that contaminates soil and water resources after its discharge from different industries. A pot experiment was conducted to determine the effects of single and/or combined application of sodium nitroprusside (SNP) (250 μM) and sodium hydrogen sulfide (NaHS) (1 mM) on growth, photosynthetic pigments, gas exchange characteristics, oxidative stress biomarkers, antioxidant machinery (enzymatic and non-enzymatic antioxidants), ion uptake, organic acid exudation, and Cr uptake of spinach (<jats:italic>Spinacia oleracea</jats:italic> L.) exposed to severe Cr stress [Cr: 0 (no Cr), 150, and 300 μM]. Our results depicted that Cr addition to the soil significantly (<jats:italic>P</jats:italic> &amp;lt; 0.05) decreased plant growth and biomass, gas exchange attributes, and mineral uptake by <jats:italic>S</jats:italic>. <jats:italic>oleracea</jats:italic> when compared to the plants grown without the addition of Cr. However, Cr toxicity boosted the production of reactive oxygen species (ROS) by increasing the content of malondialdehyde (MDA), which is the indication of oxidative stress in <jats:italic>S</jats:italic>. <jats:italic>oleracea</jats:italic>, and was also manifested by hydrogen peroxide (H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub>) content and electrolyte leakage to the membrane-bound organelles. The results showed that the activities of various antioxidative enzymes, such as superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), and the content of non-enzymatic antioxidants, such as phenolic, flavonoid, ascorbic acid, and anthocyanin, initially increased with an increase in the Cr concentration in the soil. The results also revealed that the levels of soluble sugar, reducing sugar, and non-reducing sugar were decreased in plants grown under elevating Cr levels, but the accumulation of the metal in the roots and shoots of <jats:italic>S</jats:italic>. <jats:italic>oleracea</jats:italic>, was found to be increased, and the values of bioaccumulation factor were &amp;lt;1 in all the Cr treatments. The negative impacts of Cr injury were reduced by the application of SNP and NaHS (individually or combined), which increased plant growth and biomass, improved photosynthetic apparatus, antioxidant enzymes, and mineral uptake, as well as diminished the exudation of organic acids and oxidative stress indicators in roots of <jats:italic>S</jats:italic>. <jats:italic>oleracea</jats:italic> by decreasing Cr toxicity. Here, we conclude that the application of SNP and NaHS under the exposure to Cr stress significantly improved plant growth and biomass, photosynthetic pigments, and gas exchange characteristics; regulated antioxidant defense system and essential nutrient uptake; and balanced organic acid exudation pattern in <jats:italic>S</jats:italic>. <jats:italic>oleracea</jats:italic>.</jats:p>

<jats:p>The genetic relationships among the species in <jats:italic>Scutellaria</jats:italic> genus remain unclear because of the variation in the number of species and complex trait. The usage of <jats:italic>S. baicalensis</jats:italic> and its four substitute medicinal species (<jats:italic>S. amoena</jats:italic>, <jats:italic>S. hypericifolia</jats:italic>, <jats:italic>S. likiangensis</jats:italic>, and <jats:italic>S. viscidula</jats:italic>) in traditional medicines make their specialized metabolism important in China, but interspecific genetic and chemical differences have rarely been reported for these species. In this study, the chloroplast genomes of four substitute species for <jats:italic>S. baicalensis</jats:italic> were assembled, and comparative and phylogenetic analyses were performed with these species and other <jats:italic>Scutellaria</jats:italic> relatives. In addition, metabolomics analyses were performed and the contents of the main active compounds were determined to reveal the interspecific chemical diversity of <jats:italic>S. baicalensis</jats:italic> and its four substitute species. The full lengths of their chloroplast genomes ranged from 151,574 to 151,816 bp with an average GC content of 38.34%, and a total of 113 genes were annotated. In the chloroplast genomes of <jats:italic>S. baicalensis</jats:italic> and its four substitutes, one hypervariable region (<jats:italic>petA</jats:italic>-<jats:italic>psbL</jats:italic>) is proposed as a potential DNA barcode. Phylogenetic analysis showed that the subdivision of the genus <jats:italic>Scutellaria</jats:italic> should be reconsidered. The metabolomics and content determination analyses showed that the four species exhibit a metabolism similar to that of <jats:italic>S. baicalensis</jats:italic> in different parts. Except for the roots of <jats:italic>S. likiangensis</jats:italic>, all parts of the substitute species showed high contents of baicalin. Genetic and chemical analyses of four substitute medicinal species for <jats:italic>S. baicalensis</jats:italic> were performed here for the first time, and their pharmacophylogenetic relationships were further explored, providing a scientific basis for the subsequent development of the medicinal value and resource utilization of <jats:italic>Scutellaria</jats:italic>.</jats:p>

<jats:p><jats:italic>Dacrydium pectinatum</jats:italic> de Laubenfels is a perennial dioeciously gymnosperm species dominant in tropical montane rain forests. Due to deforestation, natural disasters, long infancy, and poor natural regeneration ability, the population of this species has been significantly reduced and listed as an endangered protected plant. To better understand the female cone development in <jats:italic>D. pectinatum</jats:italic>, we examined the morphological and anatomical changes, analyzed the endogenous hormone dynamics, and profiled gene expression. The female reproductive structures were first observed in January. The morpho-histological observations suggest that the development of the <jats:italic>D. pectinatum</jats:italic> megaspore can be largely divided into six stages: early flower bud differentiation, bract primordium differentiation, ovule primordium differentiation, dormancy, ovule maturity, and seed maturity. The levels of gibberellins (GA), auxin (IAA), abscisic acid (ABA), and cytokinin (CTK) fluctuate during the process of female cone development. The female cones of <jats:italic>D. pectinatum</jats:italic> need to maintain a low level of GA<jats:sub>3</jats:sub>-IAA-ABA steady state to promote seed germination. The first transcriptome database for female <jats:italic>D. pectinatum</jats:italic> was generated, revealing 310,621 unigenes. Differential expression analyses revealed several floral (<jats:italic>MADS2</jats:italic>, <jats:italic>AGL62</jats:italic>, and <jats:italic>LFY</jats:italic>) and hormone biosynthesis and signal transduction (<jats:italic>CKX</jats:italic>, <jats:italic>KO</jats:italic>, <jats:italic>KAO</jats:italic>, <jats:italic>ABA4</jats:italic>, <jats:italic>ACO</jats:italic>, etc.) genes that could be critical for female cone development. Our study provides new insights into the cone development in <jats:italic>D. pectinatum</jats:italic> and the foundation for female cone induction with hormones.</jats:p>

<jats:p>Fragrant rice (<jats:italic>Oryza sativa</jats:italic> L.) has a high economic and nutritional value, and the application of micronutrients regulates 2-acetyl-1-pyrroline (2-AP) production, which is responsible for aroma in fragrant rice. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcript variability and proteome diversity in plants. However, no systematic investigation of AS events in response to micronutrients (Zn) has been performed in fragrant rice. Furthermore, the post-transcriptional regulation of genes involved in 2-AP biosynthesis is also not known. In this study, a comprehensive analysis of AS events under two gradients of Zn treatment in two different fragrant rice cultivars (Meixiangzhan-2 and Xiangyaxiangzhan) was performed based on RNA-seq analysis. A total of 386 and 598 significant AS events were found in Meixiangzhan-2 treated with low and high doses of Zn, respectively. In Xiangyaxiangzhan, a total of 449 and 598 significant AS events were found in low and high doses of Zn, respectively. Go analysis indicated that these genes were highly enriched in physiological processes, metabolism, and cellular processes in both cultivars. However, genotype and dose-dependent AS events were also detected in both cultivars. By comparing differential AS (DAS) events with differentially expressed genes (DEGs), we found a weak overlap among DAS and DEGs in both fragrant rice cultivars indicating that only a few genes are post-transcriptionally regulated in response to Zn treatment. We further report that Zn differentially regulates the expression of 2-AP biosynthesis-related genes in both cultivars and Zn treatment altered the editing frequency of single nucleotide polymorphism (SNPs) in the genes involved in 2-AP biosynthesis. Finally, we showed that epigenetic modifications associated with active gene transcription are generally enriched over 2-AP biosynthesis-related genes. Similar to the 2-AP pathway, we found that heavy metal transporters (genes related to silicon, iron, Zn and other metal transport) are also regulated at transcriptional and post-transcriptional levels in response to Zn in fragrant rice. Taken together, our results provide evidence of the post-transcriptional gene regulation in fragrant rice in response to Zn treatment and highlight that the 2-AP biosynthesis pathway and heavy metal transporters may also be regulated through epigenetic modifications. These findings will serve as a cornerstone for further investigation to understand the molecular mechanisms of 2-AP biosynthesis and regulation of heavy metal transporters in fragrant rice.</jats:p>

<jats:p>Powdery mildew, caused by <jats:italic>Sphaerotheca fuliginea</jats:italic> (Schlecht.) Poll., and melon aphids (<jats:italic>Aphis gossypii</jats:italic> Glover) are a typical disease and insect pest, respectively, that affect cucumber production. Powdery mildew and melon aphid often occur together in greenhouse production, resulting in a reduction in cucumber yield. At present there are no reports on the physiological and biochemical effects of the combined disease and pest infection/infestation on cucumber. This study explored how cucumbers can regulate photosynthesis, protective enzyme activity, and basic metabolism to resist the fungal disease and aphids. After powdery mildew infection, the chlorophyll and free proline contents in cucumber leaves decreased, while the activities of POD (peroxidase) and SOD (superoxide dismutase) and the soluble protein and MDA (malondialdehyde) contents increased. Cucumber plants resist aphid attack by increasing the rates of photosynthesis and basal metabolism, and also by increasing the activities of protective enzymes. The combination of powdery mildew infection and aphid infestation reduced photosynthesis and basal metabolism in cucumber plants, although the activities of several protective enzymes increased. Aphid attack after powdery mildew infection or powdery mildew infection after aphid attack had the opposite effect on photosynthesis, protective enzyme activity, and basal metabolism regulation. Azoxystrobin and imidacloprid increased the contents of chlorophyll, free proline, and soluble protein, increased SOD activity, and decreased the MDA content in cucumber leaves. However, these compounds had the opposite effect on the soluble sugar content and POD and CAT (catalase) activities. The mixed ratio of the two single agents could improve the resistance of cucumber to the combined infection of powdery mildew and aphids. These results show that cucumber can enhance its pest/pathogen resistance by changing physiological metabolism when exposed to a complex infection system of pathogenic microorganisms and insect pests.</jats:p>

<jats:p>Salinity is an abiotic stress that reduces the seed germination and productivity of wheat. The objective of this study was to assess the impact of irrigation with magnetically treated seawater on the germination, growth, certain physiological and anatomical parameters, and production attributes of wheat (<jats:italic>Triticum aestivum</jats:italic> L.) cv. Sakha 93 plants. Experiments were conducted in the Experimental Farm of the Faculty of Agriculture, Menoufia University, Egypt, during two consecutive winter seasons. Pot experiments involved ten treatments with non-magnetized and magnetized water with various degrees of salinity. Plant samples were taken 95 days after sowing. Irrigation with magnetically treated seawater was found to have beneficial effects on plant growth, water relations, biochemical characteristics, and yield components compared with untreated plants. The germination of wheat seeds increased 13% when treated with magnetic seawater. On the yield scale, the spike length was increased by 40% in season one, and 82% in season two when compared to the control, while the weight of 100 grains increased by 148% and 171%, in each season, respectively, when treated with magnetic water. The anatomical leaf and stem parameters of the plants were markedly improved by watering with magnetically treated seawater at 10 dS m<jats:sup>−1</jats:sup> compared to the control. However, the leaf water deficit, transpiration rate, and abscisic acid content in the plant shoots decreased significantly (<jats:italic>p</jats:italic> &amp;lt; 0.05). The use of magnetically treated seawater of up to 7.5 dS m<jats:sup>−1</jats:sup>, instead of tap water, is recommended due to benefits to germination and seedling parameters, growth, yield, and physiological, chemical, and anatomical characteristics. In conclusion, magnetic treatment of seawater improved germination performance, growth, and yield of wheat under saline conditions.</jats:p>

<jats:p>RNA molecules have the capacity to form a multitude of distinct secondary and tertiary structures, but only the most energetically favorable conformations are adopted at any given time. Formation of such structures strongly depends on the environment and consequently, these structures are highly dynamic and may refold as their surroundings change. Temperature is one of the most direct physical parameters that influence RNA structure dynamics, and in turn, thermosensitive RNA structures can be harnessed by a cell to perceive and respond to its temperature environment. Indeed, many thermosensitive RNA structures with biological function have been identified in prokaryotic organisms, but for a long time such structures remained elusive in eukaryotes. Recent discoveries, however, reveal that thermosensitive RNA structures are also found in plants, where they affect RNA stability, pre-mRNA splicing and translation efficiency in a temperature-dependent manner. In this minireview, we provide a short overview of thermosensitive RNA structures in prokaryotes and eukaryotes, highlight recent advances made in identifying such structures in plants and discuss their similarities and differences to established prokaryotic RNA thermosensors.</jats:p>

<jats:p>Echinatin and licochalcone A (LCA) are valuable chalcones preferentially accumulated in roots and rhizomes of licorice (<jats:italic>Glycyrrhiza inflata</jats:italic>). The licorice chalcones (licochalcones) are valued for their anti-inflammatory, antimicrobial, and antioxidant properties and have been widely used in cosmetic, pharmaceutical, and food industries. However, echinatin and LCA are accumulated in low quantities, and the biosynthesis and regulation of licochalcones have not been fully elucidated. In this study, we explored the potential of a R2R3-MYB transcription factor (TF) <jats:italic>AtMYB12</jats:italic>, a known regulator of flavonoid biosynthesis in <jats:italic>Arabidopsis</jats:italic>, for metabolic engineering of the bioactive flavonoids in <jats:italic>G. inflata</jats:italic> hairy roots. Overexpression of <jats:italic>AtMYB12</jats:italic> in the hairy roots greatly enhanced the production of total flavonoids (threefold), echinatin (twofold), and LCA (fivefold). RNA-seq analysis of <jats:italic>AtMYB12</jats:italic>-overexpressing hairy roots revealed that expression of phenylpropanoid/flavonoid pathway genes, such as <jats:italic>phenylalanine ammonia-lyase</jats:italic> (<jats:italic>PAL</jats:italic>), <jats:italic>chalcone synthase</jats:italic> (<jats:italic>CHS</jats:italic>), and <jats:italic>flavanone 3’-hydroxylase</jats:italic> (<jats:italic>F3’H</jats:italic>), is significantly induced compared to the control. Transient promoter activity assay indicated that AtMYB12 activates the <jats:italic>GiCHS1</jats:italic> promoter in plant cells, and mutation to the MYB-binding motif in the <jats:italic>GiCHS1</jats:italic> promoter abolished activation. In addition, transcriptomic analysis revealed that <jats:italic>AtMYB12</jats:italic> overexpression reprograms carbohydrate metabolism likely to increase carbon flux into flavonoid biosynthesis. Further, AtMYB12 activated the biotic defense pathways possibly by activating the salicylic acid and jasmonic acid signaling, as well as by upregulating WRKY TFs. The transcriptome of <jats:italic>AtMYB12</jats:italic>-overexpressing hairy roots serves as a valuable source in the identification of potential candidate genes involved in LCA biosynthesis. Taken together, our findings suggest that <jats:italic>AtMYB12</jats:italic> is an effective gene for metabolic engineering of valuable bioactive flavonoids in plants.</jats:p>

<jats:p>Plant architecture, flowering time and maturity traits are important determinants of yield and fiber quality of cotton. Genetic dissection of loci determining these yield and quality components is complicated by numerous loci with alleles conferring small differences. Therefore, mapping populations segregating for smaller numbers and sizes of introgressed segments is expected to facilitate dissection of these complex quantitative traits. At an advanced stage in the development of reciprocal advanced backcross populations from crosses between elite <jats:italic>Gossypium hirsutum</jats:italic> cultivar ‘<jats:italic>Acala Maxxa</jats:italic>’ (GH) and <jats:italic>G. barbadense</jats:italic> ‘<jats:italic>Pima S6</jats:italic>’ (GB), we undertook mapping of plant architectural traits, flowering time and maturity. A total of 284 BC<jats:sub>4</jats:sub>F<jats:sub>1</jats:sub> and BC<jats:sub>4</jats:sub>F<jats:sub>2</jats:sub> progeny rows, 120 in GH and 164 in GB background, were evaluated for phenotype, with only 4 and 3 (of 7) traits showing significant differences among progenies. Genotyping by sequencing yielded 3,186 and 3,026 SNPs, respectively, that revealed a total of 27 QTLs in GH background and 22 in GB, for plant height, days to flowering, residual flowering at maturity and maturity. More than of 90% QTLs identified in both backgrounds had small effects (%PV &amp;lt; 10), supporting the merit of this population structure to reduce background noise and small effect QTLs. Germplasm developed in this study may serve as potential pre-breeding material to develop improved cotton cultivars.</jats:p>

<jats:p>Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (<jats:ext-link>https://plamorph.sysbio.ru/ciscross/</jats:ext-link>) that gives more flexibility in the analysis of potential upstream TF regulators for <jats:italic>Arabidopsis thaliana</jats:italic> genes.</jats:p>