Unveiling terahertz wave stress effects and mechanisms in Pinellia ternata: Challenges, insights, and future directions.

This review aims to elucidate the intricate effects and mechanisms of terahertz (THz) wave stress on Pinellia ternata, providing valuable insights into plant responses. The primary objective is to highlight the imperative for future research dedicated to comprehending THz wave impacts across plant structures, with a specific focus on the molecular intricacies governing root system structure and function, from shoots to roots. Notably, this review highlights the accelerated plant growth induced by THz waves, especially in conjunction with other environmental stressors, and the subsequent alterations in cellular homeostasis, resulting in the generation of reactive oxygen species (ROS) and an increase in brassinosteroids. Brassinosteroids are explored for their dual role as toxic by-products of stress metabolism and vital signal transduction molecules in plant responses to abiotic stresses. The paper further investigates the spatio-temporal regulation and long-distance transport of phytohormones, including growth hormone, cytokinin, and abscisic acid (ABA), which significantly influence the growth and development of P. ternata under THz wave stress. With a comprehensive review of Reactive oxygen species (ROS) and Brassinosteroid Insensitive (BRI) homeostasis and signalling under THz wave stress, the article elucidates the current understanding of BRI involvement in stress perception, stress signalling, and domestication response regulation. Additionally, it underscores the importance of spatio-temporal regulation and long-distance transport of key plant hormones, such as growth hormone, cytokinin, and ABA, in determining root growth and development under THz wave stress. The study of how plants perceive and respond to environmental stresses holds fundamental biological significance, and enhancing plant stress tolerance is crucial for promoting sustainable agricultural practices and mitigating the environmental burdens associated with low-tolerance crop cultivation.

Transcriptomic profiling of adding cobalt chloride to improve dendrobine-type total alkaloid production.

Trichoderma longibrachiatum UN32 is known for its efficient production of dendrobine-type total alkaloids (DTTAs). This study aimed to determine the optimal medium composition for the UN32 strain using response surface methodology. Key factors, including glucose, beef extract, and CoCl2, were selected through the Plackett-Burman design. Subsequently, a factorial optimization approach was employed using the steepest ascent design, and 17 trial sets were completed via the Box-Behnken design. The optimal medium composition was found to consist of 29.4 g/L of glucose, 17.3 g/L of beef extract, and 0.28 mmol/L of CoCl2. This optimized medium resulted in an impressive 80.8% increase in mycelial dry weight (reaching 12.303 g/L) and a substantial 76.4% boost in DTTA production (reaching 541.63 ± 46.95 µg). Furthermore, the fermentation process was scaled up to a 5-L bioreactor, leading to a DTTA production approximately 1.95 times than the control. Transcriptome analysis of strain UN32 in response to CoCl2 supplementation revealed significant changes in the expression of critical genes associated with the TCA cycle and L-valine, L-leucine, and L-isoleucine biosynthesis changed. These alterations resulted in a heightened influx of acetyl-CoA into DTTA production. Additionally, the expression of genes related to antioxidant enzymes was modified to maintain homeostasis of reactive oxygen species (ROS). A potential mechanism for the accumulation of DTTAs based on ROS as a signal transduction was proposed. These findings provide valuable insights into the regulatory mechanisms of DTTA biosynthesis, potentially offering a method to enhance the production of secondary metabolites in the UN32 strain. KEY POINTS: • After the RSM optimization, there is a substantial increase of 80.8% in biomass production and a significant 76.4% rise in DTTA production. • Transcriptome analysis revealed that the inclusion of CoCl2 supplements resulted in an enhanced influx of acetyl-CoA. • Proposed a mechanism for the accumulation of DTTAs for the role of ROS as a signal transduction pathway.

First Report of Brown Leaf Rot Disease on Dendrobium nobile Caused by Xylaria flabelliformis in Guizhou Province, China.

Dendrobium nobile is the largest species of the Orchidaceae family and produces dendrobine, a compound with medicinal properties (Sarsaiya et al., 2020a; Sarsaiya et al., 2024; Qian et al., 2024). The accumulation of dendrobine in D. nobile is regulated by various pathogenic fungi, which directly and indirectly influence dendrobine biosynthesis (Sarsaiya et al., 2019a; Sarsaiya et al., 2019b). In a field planted with D. nobile in Guizhou Province, China, small lesions were initially observed on the upper part of the leaves from May to June 2019, which later developed into larger brown necrotic leaf lesions. Over time, these lesions greatly impacted the medicinal value (dendrobine) and productivity of the plant. A pure culture of Xylaria flabelliformis from infected wild D. nobile leaves was recovered and subsequently cultured on potato dextrose agar (PDA) at 25 °C for 5 days. Xylaria flabelliformis grew slowly and was composed of white mycelia. Colonies were initially white, with a regular margin, and formed stromata that consisted of mycelia sterilia without ascospores. We identified the strain as Xylaria flabelliformis based on its morphological characteristics (Liu et al., 2007) and by sequencing elongation factor-1α (EF-1α). The length of the DNA sequence of EF-1α that was used for the analysis of Xylaria flabelliformis was 1188 bp. BLASTx (nucleotide 6-frame translation-protein) analysis using the National Center for Biotechnology Information database showed that the obtained protein sequence (BLASTx protein accession no.: UTS95822.1, BLASTn nucleotide sequence accession no.: MW508334.1) had the highest similarity (98.21%) with the X. flabelliformis hypothetical protein (TRX95197.1) based on a thorough phylogenetic comparison with other Xylaria species. Healthy D. nobile seedlings were planted in pots and sterilized. The terminal leaves were excised from all pre-sterilised D. nobile seedlings and inoculated with Xylaria flabelliformis mycelial plugs, whereas sterile PDA plugs and moist cotton plugs were used as controls. All seedlings were maintained under optimum temperature and humidity conditions (25 °C and 80%, respectively) for seven days for observation and analysis. All experiments were performed in triplicate. After the incubation period, brown leaf rot lesions were observed for the first time on the inoculated D. nobile leaves, but no symptoms were observed on the leaves of the two control groups (sterile PDA plugs and moist cotton plugs). To complete Koch's postulates, Xylaria flabelliformis was re-isolated and identified from all diseased tissues by DNA sequencing of the EF-1α. It was determined for the first time that Xylaria flabelliformis can cause brown leaf lesions in D. nobile. Moreover, the pathogenicity of Xylaria flabelliformis in D. nobile has not been previously reported (Mead et al., 2019; Meng et al., 2019; Sarsaiya et al., 2019a; Sarsaiya et al., 2020b; Chen et al., 2023; Rinchen, 2023; Cao et al., 2024). To the best of our knowledge, this is the first report of BLRS lesions in D. nobile leaves caused by Xylaria flabelliformis in Guizhou Province, China. Identification of Xylaria flabelliformis as a pathogen of D. nobile is crucial for advancing effective management and control practices against brown leaf rot disease. This discovery provides valuable insights into the development of targeted strategies to mitigate the impact of Xylaria flabelliformis on D. nobile, safeguard medicinal properties such as dendrobine, and enhance overall productivity.

Recent Advances and New Insights in Genome Analysis and Transcriptomic Approaches to Reveal Enzymes Associated with the Biosynthesis of Dendrobine-Type Sesquiterpenoid Alkaloids (DTSAs) from the Last Decade.

Dendrobium species, which are perennial herbs widely distributed in tropical and subtropical regions, are notable for their therapeutic properties attributed to various bioactive compounds, including dendrobine-type sesquiterpenoid alkaloids (DTSAs). The objective of this review article is to provide a comprehensive overview of recent advances in the biosynthesis of DTSAs, including their extraction from Dendrobium species and endophytes, elucidation of associated genes through genomic and transcriptomic sequencing in both Dendrobium spp. and endophytes, exploration of the biosynthetic pathways of DTSAs, and drawing conclusions and outlining future perspectives in this field. Alkaloids, predominantly nitrogen-containing compounds found in medicinal orchids, include over 140 types discovered across more than 50 species. DTSAs, identified in 37 picrotoxane alkaloids, have a distinctive five-membered nitrogen heterocyclic ring. This review highlights endophytic fungi as alternative sources of DTSAs, emphasizing their potential in pharmaceutical applications when plant-derived compounds are scarce or complex. Genomic and transcriptomic sequencing of Dendrobium spp. and their endophytes has identified key genes involved in DTSAs biosynthesis, elucidating pathways such as the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways. Genes encoding enzymes, such as acetyl-CoA C-acetyltransferase and diphosphomevalonate decarboxylase, are positively associated with dendrobine production. Despite significant advancements, the complexity of terpenoid biosynthesis in different subcellular compartments remains a challenge. Future research should focus on leveraging high-quality genomic data and omics technologies to further understand and manipulate the biosynthetic pathways of DTSAs and enhance their medicinal use.

Cobalt stress enhanced dendrobine-type total alkaloids biosynthesis of Trichoderma longibrachiatum UN32 through reactive oxygen species formation.

Trichoderma longibrachiatum UN32 is a well-documented mutant strain known to produce dendrobine-type total alkaloids (DTTAs). It was serendipitously observed that the addition of Co2+ to the medium resulted in a notable enhancement in DTTAs production in the T. longibrachiatum UN32 strain, accompanied by an upregulating effect on the expression of antioxidase-related genes. Hence, the objective of the present work was to ascertain whether ROS (intracellular levels of hydrogen peroxide) induced by Co2+ treatment has a beneficial or detrimental impact on DTTAs biosynthesis. A comparison of the intracellular levels of hydrogen peroxide (H2O2) and DTTAs treated with CoCl2 and CH3COOH revealed that CoCl2 was the optimal inducer for investigating the relationship between ROS formation and DTTAs production. This was due to the observation that ROS formation was reduced by approximately 4% and DTTAs production was increased by 12.55% in comparison to the CH3COOH treatment. The physiological results revealed that the introduction of Co2+ resulted in the oxidative damage and activation of the expression of intracellular superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). Furthermore, it was confirmed that ROS induced by Co2+ was beneficial to DTTAs production by adding exogenous ROS scavengers. The inclusion of all ROS scavengers, including vitamin C, tocopherol, melatonin, mannitol, and sesamol, resulted in a reduction in ROS accumulation and a concomitant decrease in DTTAs production. Specifically, the addition of melatonin at a concentration of 0.4 mg/L demonstrated significant effects, resulting in a 32.53% (P < 0.01) decrease in ROS accumulation and a 45.22% (P < 0.01) reduction in DTTAs production. Subsequently, the timelines of accumulation of intracellular H2O2 and DTTAs content indicated that ROS are also crucial for normal fermentation without CoCl2 addition. Specifically, the proper H2O2 dose for DTTAs accumulation is between 8.82 and 18.86 µmol/g. The present study offers the initial experimental evidence indicating that CoCl2 enhance DTTAs production during the culture of T. longibrachiatum UN32 via leading an increase in intracellular ROS, which is conductive to DTTAs production and can be inhibited by the ROS scavengers. Our results provide insights into the mechanistic study of DTTAs biosynthesis.

First Report of Blight Caused by Rhizoctonia solani AG4-HGI on Pinellia ternata in Guizhou, China.

Pinellia ternata (Thumb.) has been used for over 1000 years as a traditional Chinese herbal medicine (Ying et al. 2007) and is widely cultivated in Guizhou Province, China. It is cultivated over an area of 2000 hectares, and is of great value to underdeveloped regions. In April 2020, blight was observed in a field of P. ternatain Bijie County, Guizhou Province, China (27°30'N, 105°28'E). Around 20 hectares of P. ternata were surveyed and the disease incidence ranged from 10 to 12%. The disease symptoms included light brown lesions formed on the stems near the soil line. The color of the lesions became darker, and the stems became constricted around the lesions and broke, associated with the leaf blight. To identify the causal agent of this blight, 22 diseased plants (about 30 d-old） were collected, the margins of the infected parts were cut into small pieces (5 mm) and surface disinfested with 1% NaOCl for 10 min, 75% ethanol for 30 s, and rinsed three times in sterile distilled water. The pieces were blotted dry with sterile filter paper and placed on potato dextrose agar (PDA, Hopebio, China), incubated at 28℃ in darkness until fungal hyphae growth was visible. Sixteen cultures with different morphologies were recovered from the samples. When representative isolates of each culture type were inoculated onto plants, one produced similar blight symptoms. The representative isolate was called CD-1. The colony color was first white but turned light brown after grown on PDA for 6-7 d, and produced dark brown sclerotia. The hyphae were branched at right angles, with a slight constriction at the base of the branches and a septum near the junction where the branch separates from the main hyphae. Hyphal cells were stained with 0.5% Safranin O and 3% KOH and were observed to be multinucleate. These morphological features indicated that CD-1 likely is R. solani (Sneh et al. 1991). When paired with tester strains AG1 and AG4(provided by Dr. Genhua Yang, Yunnan Agricultural University). CD-1 showed anastomosis with isolate of AG4 (Fenille et al. 2002). Genomic DNA was extracted from the isolate (Thangaraj et al. 2018) using a fungal genomic DNA extraction kit (Tiangen, China). The internal transcribed spacer (ITS) regions were amplified using the primers ITS1/ITS4 (White et al. 1990). A 535 bp fragment was amplified that showed 99% coverage and 99.4% identity with an isolate of R. solani AG4-HGI (GenBank: HG934417). The gene sequence was deposited in GenBank as accession #OL518945. Pathogenicity tests were performed using 30 d-old plants planted in sterilized soil in pots. Cut mycelial discs (diameter 6 mm) from 3-day-old PDA cultures and placed beside stems of 21 healthy plants. Nine plants treated with agar plugs were control samples. Inoculated plants were maintained at 24 ± 5℃ in a green house and watered every two days with sterilized water. Typical blight symptoms developed on the inoculated plants at d 3-5 post inoculation, whereas the control plants remained healthy. The experiments were repeated three times, and the isolates was re-isolated from the inoculated plants and identified as R. solaniAG4 by morphological features and molecular method. R. solani has been reported to cause blight of many plants such as coffee (Ren et al. 2018) and sesame (Cochran et al. 2018). To the best of our knowledge, this is the first report of R. solani AG4-HGI causing disease on P. ternate, both in China and worldwide. This finding suggests that this pathogen may cause a threat to cultivation and production of P. terenata.

Molecular Identification of Endophytic Fungi and Their Pathogenicity Evaluation Against Dendrobium nobile and Dendrobium officinale.

: Dendrobium are tropical orchid plants that host diverse endophytic fungi. The role of these fungi is not currently well understood in Dendrobium plants. We morphologically and molecularly identified these fungal endophytes, and created an efficient system for evaluating the pathogenicity and symptoms of endophytic fungi on Dendrobium nobile and Dendrobium officinale though in vitro co-culturing. ReThe colony morphological traits of Dendrobium myco-endophytes (DMEs) were recorded for their identification. Molecular identification revealed the presence of Colletotrichum tropicicola, Fusarium keratoplasticum, Fusarium oxysporum, Fusarium solani, and Trichoderma longibrachiatum. The pathogenicity results revealed that T. longibrachiatum produced the least pathogenic effects against D. nobile protocorms. In seedlings, T. longibrachiatum showed the least pathogenic effects against D. officinale seedlings after seven days. C. tropicicola produced highly pathogenic effects against both Dendrobium seedlings. The results of histological examination of infected tissues revealed that F. keratoplasticum and T. longibrachiatum fulfill Koch's postulates for the existence of endophytes inside the living tissues. The DMEs are cross-transmitted inside the host plant cells, playing an important role in plant host development, resistance, and alkaloids stimulation.

Sequence analysis of double-strand RNA6 and RNA9 from the fungus Sclerotium hydrophilum.

We have recently reported the identification of 10 double-strand RNA segments from Sclerotium hydrophilum [HZ11] mycelia and of virus-like particles isolated from the mycelia, as well as the sequences of dsRNA2 and dsRNA7. Phylogenetic analysis revealed that dsRNA2 and dsRNA7 belong to a group of unclassified viruses. In this report, we cloned and sequenced dsRNA6 and dsRNA9 from the 10 dsRNAs. We tentatively named the putative virus "Sclerotium hydrophilum virus 1", with isolates being abbreviated to ShV1, with dsRNA6 and dsRNA9 corresponding to dsRNA1 and dsRNA2, respectively, of ShV1. dsRNA1 was 1975 bp in length and encoded a putative RNA-dependent RNA polymerase (RdRp). dsRNA2 was 1728 bp and encoded a putative coat protein (CP). Phylogenetic analysis showed that the proteins encoded by dsRNA1 and dsRNA2 were highly related to known viral RdRps and CP, respectively, of viruses classified within the genus Alphapartitivirus of the family Partitiviridae. These members include Rhizoctonia solani dsRNA virus 2, Diuris pendunculata cryptic virus, and Heterobasidion partitivirus. The 5'- and 3'-untranslated regions (UTRs) of the two dsRNAs showed a high sequence identity. The 5'-UTR contained conserved sequences 5'-GAAGCAUCACUU(/G) G(/U)AGU(/A)UCGC(/U)CCA(/G) CAAUAACGAA-3' and 5'-AAAUUGAUCUUACCUCUCAC-3'. The 3'-UTR contained the conserved sequence 5'-UUGUUUU-3' and 5'-UUUA(/U)A(/C) UUAU-3'. These results indicate that dsRNA1 and dsRNA2 are phylogenetically related to members of the genus Alphapartitivirus of family Partitiviridae. We therefore propose that dsRNA1 and dsRNA2 are the genome sequences of a new partitivirus, ShV1.

Seed-borne viral dsRNA elements in three cultivated Raphanus and Brassica plants suggest three cryptoviruses.

Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these cryptoviruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed.

Differential Expression of miRNAs Under Salt Stress in Spartina alterniflora Leaf Tissues.

Coastal marsh habitats are impacted by many factors or disturbances, including habitat destruction, pollution, and the introduction of invasive species. Spartina alterniflora (S. alterniflora) is an important invasive species, accounting for a significant proportion of the invasive plants spread around the world. Salt stress is a major environmental stress factor, which affects plant growth and development. Little information is available regarding S. alterniflora microRNAs (miRNAs) which play important regulatory roles in plant growth and development. In order to detect S. alterniflora miRNAs and determine any expression differences between S. alterniflora plants cultivated on ordinary soils from the greenhouse and salty soils from Dafeng, in Jiangsu province of China, we carried out the detection and quantification of S. alterniflora miRNAs by microarray. Among the 81 miRNAs identified as significantly down- or up-regulated under the salt stress, 21 of the miRNAs represent 8 miRNA gene families in S. alterniflora. We found that miR168, miR399, miR395, miR393, miR171, miR396, miR169, and miR164 were down-regulated under salinity stress, and 60 of the miRNAs were up-regulated, which were revealed to be induced by salt stress in plants. The identification of differentially expressed novel plant miRNAs and their target genes, and the analysis of expression, provide molecular evidence for the possible involvement of miRNAs in the process of salt response and/or salt tolerance in S. alterniflora.

Bulbil initiation: a comprehensive review on resources, development, and utilisation, with emphasis on molecular mechanisms, advanced technologies, and future prospects.

Bulbil is an important asexual reproductive structure of bulbil plants. It mainly grows in leaf axils, leaf forks, tubers and the upper and near ground ends of flower stems of plants. They play a significant role in the reproduction of numerous herbaceous plant species by serving as agents of plant propagation, energy reserves, and survival mechanisms in adverse environmental conditions. Despite extensive research on bulbil-plants regarding their resources, development mechanisms, and utilisation, a comprehensive review of bulbil is lacking, hindering progress in exploiting bulbil resources. This paper provides a systematic overview of bulbil research, including bulbil-plant resources, identification of development stages and maturity of bulbils, cellular and molecular mechanisms of bulbil development, factors influencing bulbil development, gene research related to bulbil development, multi-bulbil phenomenon and its significance, medicinal value of bulbils, breeding value of bulbils, and the application of plant tissue culture technology in bulbil production. The application value of the Temporary Immersion Bioreactor System (TIBS) and Terahertz (THz) in bulbil breeding is also discussed, offering a comprehensive blueprint for further bulbil resource development. Additionally, additive, seven areas that require attention are proposed: (1) Utilization of modern network technologies, such as plant recognition apps or websites, to collect and identify bulbous plant resources efficiently and extensively; (2) Further research on cell and tissue structures that influence bulb cell development; (3) Investigation of the network regulatory relationship between genes, proteins, metabolites, and epigenetics in bulbil development; (4) Exploration of the potential utilization value of multiple sprouts, including medicinal, ecological, and horticultural applications; (5) Innovation and optimization of the plant tissue culture system for bulbils; (6) Comprehensive application research of TIBS for large-scale expansion of bulbil production; (7) To find out the common share genetics between bulbils and flowers.

Enhancing dendrobine production in Dendrobium nobile through mono-culturing of endophytic fungi, Trichoderma longibrachiatum (MD33) in a temporary immersion bioreactor system.

Introduction: Dendrobine, a valuable alkaloid found in Dendrobium nobile, possesses significant pharmaceutical potential. Methods: In this study, we explored innovative approaches to enhance dendrobine production by utilizing endophytic fungi in a Temporary Immersion Bioreactor System (TIBS, Nanjing BioFunction Co. Ltd., China) and traditional test bottles. Dendrobine was unequivocally identified and characterised in D. nobile co-culture seedlings through UHPLC analysis and LC-MS qTOF analysis, supported by reference standards. Results: The CGTB (control group) and EGTB (experimental group) 12-month-old D. nobile seedlings exhibited similar peak retention times at 7.6±0.1 minutes, with dendrobine identified as C16H25NO2 (molecular weight 264.195). The EGTB, co-cultured with Trichoderma longibrachiatum (MD33), displayed a 2.6-fold dendrobine increase (1804.23 ng/ml) compared to the CGTB (685.95 ng/ml). Furthermore, a bioanalytical approach was applied to investigate the mono-culture of T. longibrachiatum MD33 with or without D. nobile seedlings in test bottles. The newly developed UHPLC-MS method allowed for dendrobine identification at a retention time of 7.6±0.1 minutes for control and 7.6±0.1 minutes for co-culture. Additionally, we explored TIBS to enhance dendrobine production. Co-culturing D. nobile seedlings with Trichoderma longibrachiatum (MD33) in the TIBS system led to a substantial 9.7-fold dendrobine increase (4415.77 ng/ml) compared to the control (454.01 ng/ml) after just 7 days. The comparative analysis of dendrobine concentration between EGTB and EGTIBS highlighted the remarkable potential of TIBS for optimizing dendrobine production. Future research may focus on scaling up the TIBS approach for commercial dendrobine production and investigating the underlying mechanisms for enhanced dendrobine biosynthesis in D. nobile. The structural elucidation of dendrobine was achieved through 1H and 13C NMR spectroscopy, revealing a complex array of proton environments and distinct carbon environments, providing essential insights for the comprehensive characterization of the compound. Discussion: These findings hold promise for pharmaceutical and industrial applications of dendrobine and underline the role of endophytic fungi in enhancing secondary metabolite production in medicinal plants.

Alteration of tomato microRNAs expression during fruit development upon Cucumber mosaic virus and Tomato aspermy virus infection.

The economic importance of Solanaceae plant species is well documented, and tomato has become a model for fleshy fruit development and ripening studies. Plant microRNAs (miRNAs) are small endogenous RNAs that are involved in a variety of activities including plant development, signal transduction and protein degradation, as well as response to environment stress and pathogen invasion. Here in this study, we aimed at quantifying the expression alterations of nine miRNAs and target mRNAs in tomato flower and fruit development upon Cucumber mosaic virus (CMV) and Tomato aspermy virus infections. Three different CMV strains CMV-Fny, CMV-FnyΔ2b and CMV-Fny-satT1 were used in our investigation, and the miRNA/mRNA expression alterations were analyzed by real-time quantitative RT-PCR. The results shown the levels of several miRNA/mRNA pairs were increased upon virus infections. However, the increased level of individual miRNA differed for different virus strains, reflecting differences in severity of symptom phenotypes. The altered expression patterns of these miRNA/mRNA pairs and their predicted functions indicate the possible roles in flower and fruit development, and provide experimental data for understanding the miRNA-mediated phenotype alterations in tomato fruit.

In silico analysis the complementarity of tomato microRNA/microRNA* sequences with Cucumber mosaic virus (CMV) genomic RNAs.

Usually, modifications in normal microRNAs (miRs)-dependent gene expression are induced in transgenic plants expressing viral silencing suppressors or in viruses-inoculated plants. These phenomena are generally interpreted as a side effect of the antiviral silencing suppression. However, it has been recently reported that certain animal miRs prevent viral infection by directly interfering with pathogen replication or by binding to viral transcripts. To investigate whether such mechanisms operate in plants, we performed in silico analysis using tomato miR/miR* sequences and genomes of Cucumber mosaic virus (CMV)-Fny (the severe strain), CMV-Q (the mild strain), the aggravated satellite RNA (satRNA) variant satT1 and the attenuated variant satYn12. Results showed that a total of 38 and 37 miR/miR* sequences could bind to genomic RNAs of CMV-Fny and CMV-Q, respectively. But only one sequence could bind to safT1 and three to satYn12. Interestingly, we found that these miRs/miR*s exhibited significant complementarity within 2a and 3a Open Reading Frames (ORFs) of CMV. And most of the sequences with potential to bind viral genomes were of miR*s, suggesting novel role of miR*s in host defense response. This finding is noteworthy as plant miR* sequences are presently thought very unstable and are not assigned with any function. Finally, we could predict targets in tomato database for the miR/miR* sequences that are highlighted in our study, most of them are involved in plant metabolism. Overall, these results shed light on the possible novel role of plant miR/miR* in antiviral defense mechanisms.

Detection of genetically modified tomato using PCR coupled with muParaflo microfluidics microarrays.

Genetically modified (GM) tomatoes have been approved for commercialization in many countries since the first GM tomato FLAVR SAVR was permitted for planting in 1994. To meet the requirement of the GM tomatoes labeling policy, in this study we firstly set up the conventional PCR and multiplex PCR detection system for screening the universal elements transformed into tomato, such as cauliflower mosaic virus 35s (CaMV 35s) promoter, nopaline synthase (nos) terminator of Agrobacterium tumefaciens, neomycinphosphotransferase (nptII) gene, and the specifically inserted heterologous DNA sequence between CaMV 35s promoter and anti-sense ethylene-forming enzyme (anti-EFE) gene in GM tomato "Huafan No. 1." Tomato lat52, mcpi, fru and apx genes were used as endogenous reference genes. Besides these, a muParaflo microfluidic microarray was also developed to screen the exogenous or endogenous genes of GM tomatoes. A total of 957 probes were designed, which can be classified into two categories according to their purpose: the first for screening GM plants from un-transgenic plants based on the common elements such as promoter, reporter and terminator genes, and the second for specific gene confirmation based on target sequences such as anti-EFE or aminocyclopropane cyclase synthase (acc) gene. To ensure the reliability of this method, different kinds of positive and negative controls (such as the probes complementary to cp gene of CaMV) were included in microarray detection system. Four tomato species were identified by means of these methods, and the results indicated that microarray is a high-throughput and more efficient screening method, which could complement PCR-based screening procedures by providing direct conclusive evidence and also may be useful to resolve masking of unknown events by known events.

Analysis of the response mechanisms of Pinellia ternata to terahertz wave stresses using transcriptome and metabolic data.

Pinellia ternata (Thunb.) Breit. (Araceae), a significant medicinal plant, has been used to treat various diseases for centuries. Terahertz radiation (THZ) is located between microwaves and infrared rays on the electromagnetic spectrum. THZ possesses low single-photon energy and a spectral fingerprint, but its effects on plant growth have not yet been investigated. The study's primary objective was to examine the transcriptome and metabolome databases of the SY line to provide a new perspective for identifying genes associated with resistance and growth promotion and comprehending the underlying molecular mechanism. Variations in the biological characteristics of P. ternata grown under control and experimental conditions were analyzed to determine the effect of THZ. Compared with the control group, phenotypic variables such as leaf length, petiole length, number of leaves, leaf petiole diameter, and proliferation coefficient exhibited significant differences. P. ternata response to THZ was analyzed regarding the effects of various coercions on root exudation. The experimental group contained considerably more sugar alcohol than the control group. The transcriptome analysis revealed 1,695 differentially expressed genes (DEGs), including 509 upregulated and 1,186 downregulated genes. In the KEGG-enriched plant hormone signaling pathway, there were 19 differentially expressed genes, 13 of which were downregulated and six of which were upregulated. In the metabolomic analysis, approximately 416 metabolites were uncovered. There were 112 DEMs that were downregulated, whereas 148 were upregulated. The P. ternata leaves displayed significant differences in phytohormone metabolites, specifically in brassinolide (BR) and abscisic acid (ABA). The rise in BR triggers alterations in internal plant hormones, resulting in faster growth and development of P. ternata. Our findings demonstrated a link between THZ and several metabolic pathway processes, which will enhance our understanding of P. ternata mechanisms.

Differential effects of Cucumber mosaic virus satellite RNAs in the perturbation of microRNA-regulated gene expression in tomato.

Viral infections generally cause disease symptoms by interfering with the microRNA (miRNA)-mediated regulation of gene expression of host plants. In tomato leaves, the accumulation levels of eleven miRNAs and ten target mRNAs were enhanced by different degrees upon Cucumber mosaic virus (CMV)-Fny and Tomato aspermy virus (TAV)-Bj infections. The ability of CMV-Fny to interfere with miRNA pathway was dramatically suppressed in the addition of the benign satellite (sat) RNA variant (satYn12), but was slightly affected when CMV-Fny was co-inoculated with the aggressive satRNA variant (satT1). In plants harboring the infection of CMV-FnyΔ2b (a CMV-Fny 2b-deletion mutant), the unaltered miRNAs and target mRNAs levels compared with mock inoculated plants indicated that 2b ORF was essential for perturbation of miRNA metabolism. When the amounts of viral open reading frames (ORFs) in these infections were quantified, we found satYn12 caused a higher reduction of CMV-Fny accumulation levels than satT1. These results indicate the complex mechanism by which satRNAs participate in CMV-tomato interaction, and suggest that the severity of disease symptoms positively correlates to some extent with the perturbation of miRNA pathway in tomato.

Analysis of tomato microRNAs expression profile induced by Cucumovirus and Tobamovirus infections.

MicroRNAs (miRNAs) are a class of small RNAs that affect the morphological and physiological development of plants. In recent years, there is accumulating evidence that miRNAs are involved in defense mechanism of host plants. Therefore, investigating the alteration of miRNAs expression profiles after virus infection will provide new insights for understanding the sophisticated virus-host plant interaction. The current miRNA sequence database (miRBase) contains more than 1669 mature plant miRNAs across 25 species, but few tomato miRNAs are reported. Here we created a microarray suitable for detection of plant miRNAs based on the conservative character of miRNAs, and a total of 105 conserved plant miRNAs were detected from tomato leaf tissues. Among them, 85% of the detected miRNAs showed significant expression alterations when infected by different strains of cucumber mosaic virus (CMV) and N5 strain of tomato mosaic virus (ToMV). Combination with their symptoms development, interferences of CMV 2b protein and alleviated/aggravated satellite RNA on host miRNA pathway were discussed, and the differences in interference mechanisms between CMV and ToMV on host miRNA pathway were compared. Our results represent the comprehensive investigation of tomato miRNAs on a genome scale thus far and provide information to study the interaction between plant viruses and host plants.

Transcriptome Analysis of Dendrobine Biosynthesis in Trichoderma longibrachiatum MD33.

Dendrobine is a representative component of Dendrobium nobile, and its pharmacological effects have been extensively studied. Trichoderma longibrachiatum MD33 was isolated from the stem of Dendrobium nobile which can produce dendrobine. In order to understand the effect of Methyl Jasmonate (MeJA) on the production of dendrobine, transcriptome analysis was performed after MeJA treatment in the MD33 and control groups. The dendrobine production of MeJA (20 µmol/L) treatment group was 44.6% higher than that of control. In this study, the RNA sequencing technology was applied, a total of 444 differentially expressed genes (DEGs) in the control and MeJA treatment groups, including 226 up-regulated genes and 218 down-regulated genes. The Kyoto Encyclopedia of Genes and Genomes annotation showed that numbers of DEGs were associated with the putative alkaloid biosynthetic pathway in T Trichoderma longibrachiatum MD33. Several MVA pathway enzyme-coding genes (isopentenyl-diphosphate Delta-isomerase, iphosphomevalonate decarboxylase and farnesyl diphosphate synthase) were found to be differentially expressed, suggesting an active precursor supply for alkaloid biosynthesis after MeJA treatment, in other wise, dendrobine may synthesis through the MVA pathway in MD33. Numerous MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the dendrobine biosynthetic pathway of T. longibrachiatum MD33. Furthermore, several MeJA-induced transcription factors (TFs) encoding genes were identified, suggesting a complex genetic network affecting the dendrobine in T. longibrachiatum MD33. These findings reveal the regulation mechanism underlying the MeJA-induced accumulation of dendrobine in T. longibrachiatum MD33.