Plant Responses Research Articles

Inoculation with arbuscular mycorrhizal fungi improves plant biomass and nitrogen and phosphorus nutrients: a meta-analysis

Arbuscular mycorrhizal fungi (AMF) have profound effects on plant growth and nitrogen (N) and phosphorus (P) nutrition. However, a comprehensive evaluation of how plant N and P respond to AMF inoculation is still unavailable. Here, we complied data from 187 original researches and carried out a meta-analysis to assess the effects of AMF inoculation on plant growth and N and P nutrition. We observe overall positive effects of AMF inoculation on plant performance. The mean increases of plant biomass, N concentration, P concentration, N and P uptake of whole plant are 47%, 16%, 27%, 67%, and 105%, respectively. AMF inoculation induces more increases in plant concentrations and storage of P than N. Plant responses to AMF inoculation are substantially higher with single AMF species than with mixed AMF species, in laboratory experiments than in field experiments, and in legumes than in non-legumes. The response ratios of plant N and P nutrition are positively correlated with AMF colonization rate, N addition, P addition, and water condition, while unvaried with experiment duration. The biggest and smallest effect sizes of AMF inoculation on plant performance are observed in the application of nitrate and ammonium, respectively. Accordingly, this meta-analysis study clearly suggests that AMF inoculation improves both plant N and P nutrients and systematically clarifies the variation patterns in AMF effects with various biotic and abiotic factors. These findings highlight the important role of AMF inoculation in enhancing plant N and P resource acquisitions and provide useful references for evaluating the AMF functions under the future global changes.

Efficacy of nano urea in replacing conventional nitrogen application and its effect on fruit quality in strawberry

In a study conducted on strawberry cv. Winter Dawn, the combined application of nano urea and Azotobacter was investigated for its impact on quality and biochemical attributes under protected cultivation. The findings revealed a noteworthy response of strawberry plants to foliar nano applications compared to conventional soil application of urea. Despite the lower nitrogen dosage associated with nanoparticle supplementation, strawberries with nanoparticles exhibited significant improvements in qualitative and biochemical parameters. These results underscore the potential of urea nanoparticles as a viable nitrogen source, advocating for alternative approaches to nitrogen fertilization. By fine-tuning the dosage ratio, this strategy shows promise in fostering a more environmentally friendly, sustainable and modern method for cultivating strawberries. The enhanced quality and biochemical attributes observed in strawberries treated with nano urea highlight the efficacy of this innovative approach in optimizing plant growth and productivity. Furthermore, the utilization of nano urea in combination with Azotobacter demonstrates synergistic effects, potentially enhancing nutrient uptake and utilization efficiency in plants. This holistic approach improves crop quality and reduces the environmental impact associated with traditional fertilization methods. In conclusion, the findings of this study support the adoption of urea nanoparticles as a valuable tool in strawberry cultivation, offering a pathway towards sustainable agricultural practices. Future research efforts should focus on optimizing application protocols and assessing long-term effects to fully exploit the potential of nano-based fertilizers for strawberry.

Phenological response of plants of different biomorphs to climate change in Western Siberia

Phenological response of plants of different biomorphs to climate change in Western Siberia

CaARP1/CaSGT1 Module Regulates Vegetative Growth and Defense Response of Pepper Plants against Phytophthora capsici

Pepper (Capsicum annuum L.) suffers severe quality and yield loss from oomycete diseases caused by Phytophthora capsici. CaSGT1 was previously determined to positively regulate the immune response of pepper plants against P. capsici, but by which mechanism remains elusive. In the present study, the potential interacting proteins of CaSGT1 were isolated from pepper using a yeast two-hybrid system, among which CaARP1 was determined to interact with CaSGT1 via bimolecular fluorescence complementation (BiFC) and microscale thermophoresis (MST) assays. CaARP1 belongs to the auxin-repressed protein family, which is well-known to function in modulating plant growth. The transcriptional and protein levels of CaARP1 were both significantly induced by infection with P. capsici. Silencing of CaARP1 promotes the vegetative growth of pepper plants and attenuates its disease resistance to P. capsici, as well as compromising the hypersensitive response-like cell death in pepper leaves induced by PcINF1, a well-characterized typical PAMP from P. capsici. Chitin-induced transient expression of CaARP1 in pepper leaves enhanced its disease resistance to P. capsici, which is amplified by CaSGT1 co-expression as a positive regulator. Taken together, our result revealed that CaARP1 plays a dual role in the pepper, negatively regulating the vegetative growth and positively regulating plant immunity against P. capsici in a manner associated with CaSGT1.

Glycerophosphodiester phosphodiesterase 1 mediates G3P accumulation for Eureka lemon resistance to citrus yellow vein clearing virus

Abstract Glycerophosphodiester phosphodiesterase 1 (GDPD1) plays an important function in the abiotic stress responses and participates in the accumulation of sn-glycerol-3-phosphate (G3P) in plants, which is key to plant systemic acquired resistance (SAR). However, the role of GDPD1 in plant responses to biotic stress remains poorly understood. This study characterized the antivirus function of the GDPD1 gene (designated as ClGDPD1) from Eureka lemon. ClGDPD1 is located in the membrane and endoplasmic reticulum, where it interacts with the citrus yellow vein clearing virus (CYVCV) coat protein (CP). Compared to individually express ClGDPD1 or co-expressed ClGDPD1 + CP140-326, transiently co-expressed ClGDPD1 + CP or ClGDPD1 + CP1-139 significantly up-regulated the key substance contents and genes expression involved in glycerophospholipid metabolism. Over-expression of ClGDPD1 significantly facilitated the accumulation of G3P, up-regulated the expression of SAR-related genes, and increased the resistance of transgenic Eureka lemon to CYVCV infection. Furthermore, exogenous glycerol treatment and over-expression of ClGPDH increased the G3P content and reduced CYVCV titers in plants or hairy roots. These results indicated that the enhanced resistance of ClGDPD1 transgenic Eureka lemon to CYVCV may be due to facilitating G3P accumulation through the interaction of ClGDPD1 with CP. Our findings provide novel insights into the role of ClGDPD1 as an important regulatory center in mediating the citrus defense response to viral infections.

Indiferentní reakce sazenic borovice lesní a buku lesního ošetřených hydroabsorbenty

Super-absorbents are expected to amend soils as they are capable of retaining water, which turns dry loose powdery substances (also capsule) into hydrogel. These were applied to prevent an artificial regeneration failure due to drought events. Four commercially-available products were mixed with soil from planting holes (the capsule was put to the soil) in order to support bare-root Scots pine and European beech seedlings after a spring planting on eleven clear-cut sites in 2020–2021. The plantations were designed as rows with 4 × 150 plants treated with four hydrogels plus 150 plants without hydrogel as a control. The performance evaluation of new plantations was based on attributes such as mortality/survival and relative height and root-collar diameter increments. The plants, which lost their initial size, due to pine weevil damage, dry tops and damage by game, were excluded from the evaluation. Besides the plant response to the applied super-absorbents, the planting operations were evaluated from economic point of view. The 2020 plantations showed higher mortality than 2021 ones; both years showed an excessive loss. The hydrogels did not help the plants to survive better compared to control and growth data also showed ambiguous results. Therefore, from commercial perspective, the application of all tested super-absorbents just increased the renewal costs.

Genome-wide analysis of glutathione S-transferase genes in four Prunus species and the function of PmGSTF2, activated by PmMYBa1, in regulating anthocyanin accumulation in Prunus mume

Glutathione S-transferases (GSTs) are proteases with multiple physiological functions and play an important role in plant responses to abiotic stresses. Nevertheless, there is a paucity of systematic research on GST genes in Prunus genus. Here, 330 GST genes in four Prunus species were identified for the first time and classified into eight subgroups based on protein sequence and conserved structure, among which Tau subfamily genes had the largest number. The amino acid lengths of GST-encoded proteins in the four species ranged from 66 to 1152 aa, most of which were soluble proteins and located in the cytoplasm and chloroplasts. The GST family was propelled by tandem duplications, yet robust purifying selection constrained its divergence. Conserved motif and domain analysis revealed that the majority of PmGSTs exhibited a highly conserved GST-N structure. The expression pattern of PmGSTs exhibited tissue specificity and spatiotemporal specificity. qRT-PCR validated the transcriptome results and 11 genes were differentially expressed in varieties with different flower and stem colors. In addition, we discovered an anthocyanin-related gene PmGSTF2, which can effectively restore the anthocyanin and proanthocyanidin deficiency-related phenotypes of the Arabidopsis tt19 mutant. Recombinant PmGSTF2 enhanced the water solubility of cyanidin and cyanidin-3-O-glucoside in vitro. Moreover, PmMYBa1 could directly bind to the promoter of PmGSTF2 and activate its expression. The findings revealed that GSTs were preserved in Prunus species and that PmGSTF2 was critical in regulating anthocyanin accumulation.

Plant Theory

Abstract Over a hundred years after the publication of the scientist Jagadish Chandra Bose’s 1922 Abyakta, a book of essays in Bangla where he writes about his experiments on plant life, the response of plants to external stimuli, particularly electrical energy, a nervous system in plants, and his work towards revealing what he calls ‘torulipi’, a plant script, so as to be able to prove that plants were indeed living beings, scientists are now proving many of the Indian scientist’s findings. Simultaneous with this has been a public enthusiasm for the work of writers and artists that feature speculation over, and the subsequent creation of, a plant script. This review of works published in 2023 considers two key publications that illuminate the prescience of Bose’s thought for the contemporary investment in the plant humanities: Katie Holten’s edited anthology The Language of Trees and the spring 2023 special issue of Orion on ‘The Language of Nature’. This review therefore focuses on literature about the plant script while also recording and contextualizing the zeitgeist that compels and indulges such an imagining.

Enhanced detection of glyphosate with a Co-MOF integrated opto-electrochemical sensor

Abstract This study presents a new method for detecting the organophosphorus pesticide glyphosate using advanced scanning electrodes (SPE) and enhanced fluorescence. Metal-organic frameworks from cobalt ions were synthesized using a solvothermal method. It is characterized using Raman spectroscopy, FT-IR, and X-ray diffraction techniques. The electrocatalytic behavior of the materials was studied using electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). Differential pulse voltammetry (DPV) examined the positive response of plants to glyphosate over a concentration range of 0.55–5.95 mM with a detection limit of 0.334 mM. The fluorescence enhancement ranges from 0.07 mM to 0.67 mM, and the detection limit is 0.0998 mM. Additionally, the selectivity of the proposed opto-electrochemical sensor was evaluated. This selection demonstrates the sensor's ability to detect glyphosate in complex wastewater matrices. This has important implications for environmental monitoring. By addressing glyphosate contamination, the sensor could significantly advance ecological remediation and monitoring strategies. The selectivity, sensitivity, and ability to operate under harsh conditions represent a significant advance in the development of efficient and reliable glyphosate technology for wastewater treatment and environmental protection. In real-sample matrices, the suggested sensor showed a good recovery of the pesticide that had been spiked.

Stress Responses to Bark Beetle Infestations among Pine (Pinus sylvestris), Fir (Abies alba), and Beech (Fagus sylvatica) Trees

Insect infestation triggers multiple defense responses in plants, both locally at the infection site and systemically throughout the plant, including the production of feeding deterrents, toxins, defensive proteins, enzymes, and secondary metabolites. Our study aimed to compare the endogenous levels of antioxidative enzymes, photosynthetic pigments, phytohormones, total phenols, and flavonoids in bark-beetle-infested and uninfested trees. We evaluated the surviving trees in bark-beetle-infested stands, assessing both the condition and defense of uninfested and infested beech (Fagus sylvatica), pine (Pinus sylvestris), and fir (Abies alba) trees. Sampling was performed at six affected sites in the Czech Republic, targeting trees that were resilient to significant health deterioration caused by abiotic and biotic factors. The results showed different levels of most of the measured compounds in the three species. Among all the tested species, photosynthetic pigment levels showed the strongest association with infestation status, which was generally lower in the infested plants. For chlorophyll a, extremely significant reductions were observed from 123 ± 20.6 to 101 ± 17.9 μg/g dry weight (DW) in pine, from 231 ± 33.1 to 199 ± 22.2 μg/g DW in beech, and from 60 ± 5.66 to 51.3 ± 6.27 μg/g DW in fir. In contrast, enzymatic activities indicated only isolated instances of significant association, whereas antioxidative properties (total phenolic content, flavonoids, and 2,2-diphenyl-1-picrylhydrazyl radical scavenging capacity) were not significantly associated with infestation status. There was a statistically significant increase in glutathione reductase activity in infested fir and pine trees. However, this difference was not statistically significant in beech. In contrast, a significant increase in superoxide dismutase activity was detected in infected beech trees. Phytohormones have emerged as the most diverse group of analyzed compounds. Cytokinins were the most distinct, with many of them being significantly increased in infested pines, whereas both beech and fir showed only one significant association. Additionally, derivatives of jasmonic acid also showed a distinct pattern of change associated with bark beetle infestation, with the levels of three out of the four analyzed jasmonates being significantly decreased in infested pines, whereas no effects were observed in beeches and firs. Notably, many phytohormones were significantly elevated in the infested pine, whereas both beech and fir exhibited only one significant association. Overall, the data showed that pines responded differently to bark beetles than to beeches or firs. The greatest changes in phytohormones were observed in pine, whereas the most significant changes in photosynthetic pigments were observed in beech and fir trees.

ARR1 and ARR12 modulate arsenite toxicity responses in Arabidopsis roots by transcriptionally controlling the actions of NIP1;1 and NIP6;1.

Cytokinin is central to coordinating plant adaptation to environmental stresses. Here, we first demonstrated the involvement of cytokinin in Arabidopsis responses to arsenite [As(III)] stress. As(III) treatment reduced cytokinin contents, while cytokinin treatment repressed further primary root growth in Arabidopsis plants under As(III) stress. Subsequently, we revealed that the cytokinin signaling members ARR1 and ARR12, the type-B ARABIDOPSIS RESPONSE REGULATORs, participate in cytokinin signaling-mediated As(III) responses in plants as negative regulators. A comprehensive transcriptome analysis of the arr1 and arr12 single and arr1,12 double mutants was then performed to decipher the cytokinin signaling-mediated mechanisms underlying plant As(III) stress adaptation. Results revealed important roles for ARR1 and ARR12 in ion transport, nutrient responses, and secondary metabolite accumulation. Furthermore, using hierarchical clustering and regulatory network analyses, we identified two NODULIN 26-LIKE INTRINSIC PROTEIN (NIP)-encoding genes, NIP1;1 and NIP6;1, potentially involved in ARR1/12-mediated As(III) uptake and transport in Arabidopsis. By analyzing various combinations of arr and nip mutants, including high-order triple and quadruple mutants, we demonstrated that ARR1 and ARR12 redundantly function as negative regulators of As(III) tolerance by acting upstream of NIP1;1 and NIP6;1 to modulate their function in arsenic accumulation. ChIP-qPCR, EMSA, and transient dual-LUC reporter assays revealed that ARR1 and ARR12 transcriptionally activate the expression of NIP1;1 and NIP6;1 by directly binding to their promoters and upregulating their expression, leading to increased arsenic accumulation under As(III) stress. These findings collectively provide insights into cytokinin signaling-mediated plant adaptation to excessive As(III), contributing to the development of crops with low arsenic accumulation.

Biochemical Defence of Plants against Parasitic Nematodes

Plant parasitic nematodes (PPNs), such as Meloidogyne spp., Heterodera spp. and Pratylenchus spp., are obligate parasites on a wide range of crops, causing significant agricultural production losses worldwide. These PPNs mainly feed on and within roots, impairing both the below-ground and the above-ground parts, resulting in reduced plant performance. Plants have developed a multi-component defence mechanism against diverse pathogens, including PPNs. Several natural molecules, ranging from cell wall components to secondary metabolites, have been found to protect plants from PPN attack by conferring nematode-specific resistance. Recent advances in omics analytical tools have encouraged researchers to shed light on nematode detection and the biochemical defence mechanisms of plants during nematode infection. Here, we discuss the recent progress on revealing the nematode-associated molecular patterns (NAMPs) and their receptors in plants. The biochemical defence responses of plants, comprising cell wall reinforcement; reactive oxygen species burst; receptor-like cytoplasmic kinases; mitogen-activated protein kinases; antioxidant activities; phytohormone biosynthesis and signalling; transcription factor activation; and the production of anti-PPN phytochemicals are also described. Finally, we also examine the role of epigenetics in regulating the transcriptional response to nematode attack. Understanding the plant defence mechanism against PPN attack is of paramount importance in developing new, effective and sustainable control strategies.

Factors and effects of inter-individual variability in silver birch phenology using dense LiDAR time-series

Comprehending and quantifying local variability in plant phenology, alongside its impacts on tree growth, is challenging due to spatially and temporally heterogeneous environmental factors that interact to affect phenological events and periods. Although previous studies have focused on the climatic factors driving phenological events at the stand level, the influences of competition, neighborhood characteristics, species richness, and water availability on plant phenology remain unclear. In the present paper, we used hourly terrestrial LiDAR surveys performed between April 2020 and April 2021 to investigate the influence of local factors (neighborhood and topography) on the phenology of silver birch trees (Betula pendula Roth.). We also examined how phenological events affect growth in tree height and crown area. All response and explanatory variables were estimated using LiDAR time-series data and a field survey campaign. Our findings demonstrate a high within-species variability in plant phenology that is controlled by biotic and abiotic characteristics of the ecosystem. We found that between tree variation in leaf burst, completion of the leaf growth and length of canopy growth period were affected by tree size, neighborhood species richness, level of suppression and competition, which potentially indicate plant responses to light availability. The beginning of senescence, completion of leaf drop, and length of autumn phenology were mostly affected by topographic water index, which reflects water availability and can be linked to nutrient availability and exposure to wind. Furthermore, we demonstrated that an earlier leaf burst, and delayed beginning of senescence were associated with larger absolute growth in canopy area but found no clear relationship between height growth and phenology. Our study highlights the capability of dense, high-quality LiDAR time-series to detect significant phenological variation among individuals of the same species within the same locality, demonstrating the potential of LiDAR time-series as a tool for understanding phenology and its impacts.

Genome-wide identification of m6A-related gene family and the involvement of TdFIP37 in salt stress in wild emmer wheat.

The genomic organization, phylogenetic relationship, expression patterns, and genetic variations of m6A-related genes were systematically investigated in wild emmer wheat and the function of TdFIP37 regulating salt tolerance was preliminarily determined. m6A modification is one of the most abundant and crucial RNA modifications in eukaryotics, playing the indispensable role in growth and development as well as stress response in plants. However, its significance in wild emmer wheat remains elusive. Here, a genome-wide search of m6A-related genes was conducted in wild emmer wheat to obtain 64 candidates, including 21 writers, 17 erasers, and 26 readers. Phylogenetic and collinearity analysis demonstrated that segmental duplication and polyploidization contributed mainly to the expansion of m6A-related genes in wild emmer. A number of cis-acting elements involving in stress and hormonal regulation were found in the promoter regions of them, such as MBS, LTR, and ABRE. Genetic variation of them was also investigated using resequencing data and obvious genetic bottleneck was occurred on them during wild emmer wheat domestication process. Furthermore, the salt-responsive candidates were investigated through RNA-seq data and qRT-PCR validation using the salt-tolerant and -sensitive genotypes and the co-expression analysis showed that they played the hub role in regulating salt stress response. Finally, the loss-function mutant of Tdfip37 displayed the significantly higher salt-sensitive compared to WT and then RNA-seq analysis demonstrated that FIP37 mediated the MAPK pathway, hormone signal transduction, as well as transcription factor to regulate salt tolerance. This study provided the potential m6A genes for functional analysis, which will contribute to better understand the regulatory roles of m6A modification and also improve the salt tolerance from the perspective of epigenetic approach in emmer wheat and other crops.

Reducing red light proportion in full-spectrum LEDs enhances runner plant propagation by promoting the growth and development of mother plants in strawberry

Full-spectrum light-emitting diodes (LEDs) have gradually replaced narrow-spectrum LEDs and are widely used in plant factories with artificial lighting (PFALs). However, the specific effect of LED light quality on dry mass allocation in runner plant propagation remains unclear. Hence, we cultivated “Akihime” strawberries as mother plants for 115 days to conduct runner plant propagation experiment under white LEDs (W100), white and red LEDs (W84R16 and W55R45), red and blue LEDs (RB100), and red, blue and green LEDs (RB80G20) in PFALs, and determined key factors affecting dry mass accumulation and allocation among mother plants and runner plants based on growth component analysis. The results showed that the net photosynthetic rate and total leaf area in mother plants in W100 increased by 11% and 31%, respectively, compared with W55R45. In comparison to W84R16 and W55R45, W100 increased the dry mass (23%–30%) of runner plants mainly by increasing the total dry mass (TDM) (23%) of strawberry plants, without significantly affecting the fraction of dry mass partitioning to runner plants. However, the number of runners in W55R45 was 5.1 per plant, representing only 78% of that in W100. Compared with RB100, RB80G20 significantly increased the number of runner plants and runner numbers by 16% and 19% to 13.0 per plant and 5.8 per plant, respectively. The partial replacement of blue light with green light in RB80G20 induced a shade avoidance response in runner plants, resulting in a 55% increase in the total leaf area of runner plants compared with RB100. Data from growth component analysis showed that compared with red and blue LEDs, white LEDs increased the TDM of runner plants by 83% by increasing the plant TDM accumulation (44%) and the fraction of dry mass partitioning to runner plants (37%). Additionally, the dry mass (g) of runner plants per mol and per kilowatt-hour under in W100 were 0.11 and 0.75, respectively, significantly higher than other treatments. Therefore, reducing red light proportion in full-spectrum LEDs is beneficial for strawberry runner plant propagation in PFALs.

Genome-wide characterization and expression analysis of WRKY transcription factors reveals biotic stress response potential mechanisms in Panax notoginseng

WRKY transcription factors (TFs), among the largest families of transcriptional regulators, are essential players in defense responses in plants. Panax notoginseng, a traditional and precious herbal medicine in China, is widely cultivated due to its excellent medicinal and edible value. However, P. notoginseng is frequently affected by various diseases (like Black blot disease, Root rot disease and Viral diseases). Therefore, the present study aimed to identify and characterize PnWRKYs in the P. notoginseng genome, reveal their structural attributes, regulatory elements, and potential functions in defense responses. 68 PnWRKY TFs that have conserved domains and different physicochemical characteristics were identified in the genome. They can be divided into four groups according to phylogenetic relationships and conserved domain structures. Furthermore, Group II WRKY TFs can be classified into five subgroups (IIa, IIb, IIc, IId, and IIe) according to their zinc finger-like motif. The PnWRKY family expands mainly via segmental duplication. Additionally, the promoter regions of PnWRKYs contain many hormone-responsive and stress-responsive elements. Expression patterns under different hormones (salicylic acid, methyl jasmonate, and melatonin) and disease (root rot disease, black blot disease, and virus disease) treatment analysis highlighted their wide involvement in plant hormone-induced disease defense responses. These findings affirmed the potential functions of PnWRKY TFs in disease-mediated defense responses and provided valuable insights for future agricultural applications.

The RNA helicase LOS4 regulates pre-mRNA splicing of key genes (EIN2, ERS2, CTR1) in the ethylene signaling pathway.

The Arabidopsis RNA helicase LOS4 plays a key role in regulating pre-mRNA splicing of the genes EIN2, CTR1, and ERS2 in ethylene signaling pathway. The plant hormone ethylene plays diverse roles in plant growth, development, and responses to stress. Ethylene is perceived by the membrane-bound ethylene receptors complex, and then triggers downstream components, such as EIN2, to initiate signal transduction into the nucleus, leading to the activation of ethylene-responsive genes. Over the past decades, substantial information has been accumulated regarding gene cloning, protein-protein interactions, and downstream gene expressions in the ethylene pathway. However, our understanding of mRNA post-transcriptional processing and modification of key genes in the ethylene signaling pathway remains limited. This study aims to provide evidence demonstrating the involvement of the Arabidopsis RNA helicase LOS4 in pre-mRNA splicing of the genes EIN2, CTR1, and ERS2 in ethylene signaling pathway. Various genetic approaches including RNAi gene silencing, CRISPR-Cas9 gene editing, and amino acid mutations were employed in this study. When LOS4 was silenced or knocked down, the ethylene sensitivity of etiolated seedlings was significantly enhanced. Further investigation revealed errors in the EIN2 pre-mRNA splicing when LOS4 was knocked down. In addition, aberrant pre-mRNA splicing was observed in the ERS2 and CTR1 genes in the pathway. Biochemical assays indicated that the los4-2 (E94K) mutant protein exhibited increased ATP binding and enhanced ATP hydrolytic activity. Conversely, the los4-1 (G364R) mutant had reduced substrate RNA binding and lower ATP binding activities. These findings significantly advanced our comprehension of the regulatory functions and molecular mechanisms of RNA helicase in ethylene signaling.

Genome architecture of the heavy metal tolerant and accumulator Hirschfeldia incana: Insights from genome sequencing, assembly, and comparative analysis

Hirschfeldia incana L., a member of the Brassicaceae family commonly found in Mediterranean regions, is known for its capacity to withstand and accumulate heavy metals, particularly lead (Pb) both in soil environments and hydroponic systems. This plant has been used as a model to study plant responses to heavy metals. Nonetheless, the molecular mechanisms underlying its tolerance and heavy metal accumulation are not fully understood, partly because of the limited knowledge about its genome. In this study, the genome of H. incana was sequenced, assembled, characterized, and annotated. Approximately 8.6 Gpb of data were generated using Oxford Nanopore Technology (ONT), resulting in a genome assembly of 390 Mb, comprising 5196 contigs with an N50 exceeding 131 kb. The genome had a BUSCO score of 97.2 %, with 38,454 genes and a repetition content of 38.25 %. Subsequently, the assembled genome was annotated using several databases including GO, InterPro, MetaCyc, PANTHER, Pfam, Reactome, SUPERFAMILY, and KEGG. This annotation yielded 22,661 GO terms and 143 KEGG maps. A comparative genomic analysis between H. incana and six Brassicaceae species (five hyperaccumulators of heavy metals and one non-hyperaccumulator) was also conducted. This analysis revealed that H. incana shares a substantial proportion of orthologous genes (89.7 % of orthogroups) with six Brassicaceae species. The generated phylogenetic tree suggests that H. incana is closely related to B. juncea, B. napus, and B. oleracea, indicating a common ancestry and potentially shared genetic factors contributing to hyperaccumulation in these species. Moreover, the copy number of twenty-nine genes involved in heavy metal tolerance and accumulation mechanisms in H. incana and six brassicaceae were assayed. This analysis revealed that H. incana and other hyperaccumulator species possess a higher copy number of genes related to heavy metal tolerance than the sensitive plant A. thaliana. Notably, the variation in gene copy numbers highlights their potential role in the adaptation of H. incana to heavy metal stress. This study provides a comprehensive genomic framework that enhance our understanding of H. incana adaptation to heavy metal stress, and offers valuable data for further genomic investigations of the molecular mechanisms of heavy metal tolerance and accumulation in plants.

Characterization and expression analysis of the MADS-box gene AGL8 in cotton: insights into gene function differentiation in plant growth and stress resistance.

AGAMOUS-LIKE 8 (AGL8) belongs to the MADS-box family, which plays important roles in transcriptional regulation, sequence-specific DNA binding and other biological processes and molecular functions. The genome of cotton, a representative polyploid plant, contains multiple AGL8 genes. However, their functional differentiation is still unclear. In this study, a comprehensive genomic analysis of AGL8 genes was conducted. Cotton AGL8s were subdivided into four subgroups (Groups 1, 2, 3, and 4) based on phylogenetic analysis, and different subgroups of AGL8s presented different characteristics, including different structures and conserved motifs. With respect to the promoter regions of the GhAGL8 genes, we successfully predicted cis-elements that respond to phytohormone signal transduction and the stress response of plants. Transcriptome data and real-time quantitative PCR validation indicated that three genes, namely, GH_D07G0744, GH_A03G0856 and GH_A07G0749, were highly induced by methyl jasmonate (MeJA), salicylic acid (SA), and abscisic acid (ABA), which indicated that they function in plant resistance to abiotic and biotic stresses. The information from the gene structure, number and types of conserved domains, tissue-specific expression levels, and expression patterns under different treatments highlights the differences in sequence and function of the cotton AGL8 genes. Different AGL8s play roles in vegetative growth, reproductive development, and plant stress resistance. These results lay a foundation for further study of GhAGL8s in cotton.

Reading m6A marks in mRNA: A potent mechanism of gene regulation in plants.

Modifications to RNA have recently been recognized as a pivotal regulator of gene expression in living organisms. More than 170 chemical modifications have been identified in RNAs, with N6-methyladenosine (m6A) being the most abundant modification in eukaryotic mRNAs. The addition and removal of m6A marks are catalyzed by methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. In addition, the m6A marks in mRNAs are recognized and interpreted by m6A-binding proteins (referred to as "readers"), which regulate the fate of mRNAs, including stability, splicing, transport, and translation. Therefore, exploring the mechanism underlying the m6A reader-mediated modulation of RNA metabolism is essential for a much deeper understanding of the epigenetic role of RNA modification in plants. Recent discoveries have improved our understanding of the functions of m6A readers in plant growth and development, stress response, and disease resistance. This review highlights the latest developments in m6A reader research, emphasizing the diverse RNA-binding domains crucial for m6A reader function and the biological and cellular roles of m6A readers in the plant response to developmental and environmental signals. Moreover, we propose and discuss the potential future research directions and challenges in identifying novel m6A readers and elucidating the cellular and mechanistic role of m6A readers in plants.