Plant Biochemical Pathways Research Articles

Plants and fungi metabolites as novel autophagy inducers and senescence inhibitors

Premature aging can be partially explained by inefficient autophagy (the process of cellular self-digestion that recycles intracellular components) and premature senescence (cease of cellular division without cell death activation). Autophagy and senescence are among the basic biochemical pathways in plants and fungi suggesting that some of their metabolites have the potential to act as autophagy inducers (AI) and senescence inhibitors (SI) and to inhibit inflammation and human aging. Several compounds have already been identified: trehalose and resveratrol are natural compounds that act as AI; flavonoids found in fruit and vegetables (curcumin, quercetin, and fisetin) are among the first SI discovered so far. New AI/SI can be identified using various approaches like hypothesis-driven approach for screening receptor agonists using an in-silico library of thousands of natural compounds; cheminformatics studies of phytochemicals using docking and molecular dynamics simulation, structure similarities/mimicry in vitro, “blind” high throughput screening (HTS) of libraries of natural metabolites against relevant models, and more. This article aims to promote the use of plant and fungi novel resources to identify bioactive molecules relevant for healthy aging based on the knowledge that plants and fungi use autophagy and senescence mechanisms for their own survival and homeostasis. As autophagy and senescence are interconnected, how drugs targeting autophagy, senescence, or both could contribute to healthy aging in humans will be speculated.

The effect of salicylic acid on the content of ascorbic acid and phenolic compounds in wheat plants

Background. Salicylic acid is an important phytohormone in plants, influencing various functions such as senescence, respiration, and stress resistance. Despite extensive studies the role of salicylic acid in stress, its effects under normal conditions are less understood. This study explores the influence of salicylic acid on the biosynthesis of important biochemical compounds such as ascorbic acid, rutin, and other phenolic compounds in wheat (Triticum aestivum L.), aiming to elucidate potential applications in agriculture. Materials and Methods. Wheat variety 'Podolyanka' was treated with 0.05 mM salicylic acid and grown under controlled conditions. Biochemical analyses were studied on 7, 10 and 20 days of growth to using the spectrophotometric method for the determination of ascorbic acid, rutin, total phenolic compounds, anthocyanins, flavonoids, and xanthones. Methods included chromatography on the plate with silicagel for rutin. Results and Discussion. Salicylic acid treatment significantly increased the ascorbic acid content in wheat shoots at all studied stages. There was also a notable increase in rutin content in the early growth phase. However, the content of other phenolic compounds, such as xanthones, generally decreased under salicylic acid treatment. Intriguingly, anthocyanin content was increased, suggesting a complex interaction within the biosynthetic pathways influenced by salicylic acid. The study also revealed correlations among different phenolic compounds, indicating intertwined metabolic pathways. Conclusion. Salicylic acid enhances the biosynthesis of specific phenolic compounds like ascorbic acid and rutin in wheat, which can have implications for agricultural practices aiming at improving plant resilience and nutritional quality. The differential impact of SA on various phenolic compounds underscores the complexity of plant biochemical pathways and highlights the need for further research to fully understand these interactions and their practical applications.

Insights into mode of action mediated responses following pharmaceutical uptake and accumulation in plants

The reuse of wastewater to meet irrigation requirements and slurries, sludges and manures as fertilisers to meet crop nutrient demands inadvertently introduces human and veterinary-use pharmaceuticals into the agro-ecosystem. This review synthesises recent research, which has observed sub-lethal effects, following pharmaceutical uptake by plants. Potential links between pharmaceutical mode of action and observed sub-lethal effects in the plant were then examined. Common receptors and biological pathways across species suggests a clear need to integrate plant cellular biology into our understanding of the impacts of pharmaceuticals on important plant functions and processes. To help prioritise future research efforts an analysis of shared mammalian and plant biochemical pathways was undertaken to identify classes of pharmaceuticals which may present a greater risk to key plant functions. These included sulfonylurea antihyperglycemics, steroids, opiods, antipsychotic phenothiazines and pharmaceuticals targeting several neurotransmitters shared between mammals and plants (including beta-blockers, antihistamines and benzodiazepines). Whilst a number of pharmaceutical induced sub-lethal effects have been observed, this review highlights the clear need to study a wider range of pharmaceuticals on a broader range of plant species, including cover crops and wild plants, under realistic exposure scenarios, to fully understand the wider implications of pharmaceutical exposure in agro-ecosystems. State-of-the art omics-techniques offer great potential to understand the mode of action of pharmaceuticals in plants and elucidate links between the pharmaceutical intended mode of action and observed plant effects. In addition, studies under co-stress from pharmaceutical exposure and other stressors such as increased temperatures, drought or pests are lacking and present an urgent research need in the face of feeding a growing population under the threats of climate change.

Activity Prediction of Various Herbicides against Honey Bee, Avian, and Multiple Human Leukemia, CNS, Ovarian, Prostate Cancer Cell Lines

Herbicides classify as chemicals targeting specific biochemical pathways in plants and may influence human or animal health according to their chemistry, concentration, environment, biological target and others. With safety concern, International Agency for Research on Cancer (IARC) classified herbicides and their metabolites as fetal developments may be a consequence of enzymatic inhibition or other mechanisms. Thirty phytotoxins were subjected to online pkCSM website, as a Quantitative Structure Activity Relationship (QSAR) prediction activity against honey bee, avian, and multiple human Leukemia, CNS, Ovarian, Prostate Cancer cell lines. Prediction outcomes were varied and influenced by chemical structure of each tested herbicide. Sulfentrazone having evidence of human non- carcinogenic character (Group E) had hepatotoxicity prediction and cancer cell lines activity less than 5 of Leukemia, CNS, Ovarian, and Prostate. Also, it had CYP1A2 inhibition, negative response of p- glycoprotein, Ames, skin sensitization, renal OCT2, and hERG. All above characters beside low intestinal absorption and Blood- Brain Barrier (BBB) presented encouraging online funding as more structurally safe having active – multiple toxicological and cellular interactions. Simetryn and Simazine that have the same core structure except (-SCH3) group replaced with chloro group gave semi identical results of many calculated characters and inactive materials to cancer cell lines and herbicide activity, honey bee and avian toxicities but not BBB, total clearance, and oral rat chronic (LOAEL) confirming structure influences upon prediction.

Profiling of Peak Intensity and Standard Deviation of Metabolites in Industrially Important Red Seaweed Gracilaria dura (Rhodophyta) by 1H NMR Spectra for Benchmarking

Mapping of regulatory components of cellular functioning by 1H NMR metabolomics has recently paved the way to study biochemical pathways in plants. Despite the enormous complexity and heterogeneity of the metabolites, the estimation of molar concentration allows for their direct quantification without calibration for individual compounds. 1H NMR spectra of near-native extracts were recorded for a large number (55 each) of wild and cultured samples of the industrially important red seaweed Gracilaria dura to obtain quantitative data of all the metabolites. Average and standard deviation of the respective classes were calculated from 1H NMR spectra wherein significant differences between wild and cultured groups were observed in the 1.56–3.50 ppm region. A significant region in the wild samples having a low average (0–0.98) and standard deviation (0.2–0.81) was 1.56–2.96 ppm representing nitrogen-containing compounds. The same region was found to have a much higher standard deviation (0.13–1.73) with average (0–2.03) in cultured samples. In comparison, sugar metabolites (triethanolamine, galactose, lactate, threonine) have a high average peak intensity and similar standard deviation across both groups of samples. This observation reveals that sugar compounds are critical in central metabolic pathways while nitrogen compounds change due to the environment. PCA analysis revealed an interpretable overview of main information enclosed in a multidimensional data set; the differences were correlated to environmental determinants, developmental, and growth states. A signature metabolite profile is presented with minor standard deviation differences between significant parts of the 1H NMR spectra, confirming its use as a rapid chemo-taxonomic tool supplementary to the conventional approach.

A Review on the Role of Silicon Treatment in Biotic Stress Mitigation and Citrus Production

This paper reviews the threat of citrus pathogens during citrus production, with a focus on two pre-harvest diseases, citrus leaf spot, caused by Alternaria alternata (Fr.) Keissl. (1912) and brown rot, caused by Phytophthora citrophthora (R.E. Sm. and E.H. Sm.) Leonian, (1906) as well as green and blue mold post-harvest disease, caused by Penicillium digitatum (Pers.) Sacc. and P. italicum Wehmer, (1894), respectively. Furthermore, it reviews the role of soluble silicon, Si nutrition in biotic stress mitigation and potential mitigation mechanisms. Previous studies on the use of Si fertilizers have focused on high accumulator Si crops. These have demonstrated the potential of Si to reduce the occurrence of biotic stresses, which takes place through both physical and biochemical mechanisms. However, few studies have demonstrated the potential of Si to mitigate biotic stress in citrus, or the mechanisms involved. There is a clear need for studies on the impact of Si on various stress biochemical pathways in plants generally, and specifically for citrus due to the huge loss caused by pre- and post-harvest pathogens. This will assist in deepening our understanding of the pathophysiology which is essential to develop resistant cultivars.

Methods for Screening Legume Crops for Abiotic Stress Tolerance through Physiological and Biochemical Approaches.

Legume crops are subjected to a wide range of abiotic stresses, which stimulate an array of physiological, biochemical, and molecular responses. However, different genotypes may exhibit significant variations between individual responses, which can determine their tolerance or susceptibility to these stresses. The present chapter suggests a broad range of assays that can help in understanding stress perception by plants at cellular and molecular levels. The genotypes may be sorted depending on their tolerance potential, by broadly analysing morphological, physiological, biochemical, and enzyme kinetics parameters. These assays are very beneficial in revealing the mechanism of stress perception and response in varied plant types, and have helped in discriminating contrasting genotypes. Here, we have described detailed protocols of assays which may be carried out to assess tolerance or susceptibility to abiotic stresses. The analysis, as a whole, can help researchers understand the effect of abiotic stresses on plant biochemical pathways, be it photosynthesis, redox homeostasis, metabolite perturbation, signaling, transcription, and translation. These protocols may be beneficial in identification of suitable donors for breeding programs, as well as for identifying promising candidate genes or pathways for developing stress tolerant legume crops through genetic engineering.

Zinc nutrition in chickpea (Cicer arietinum): a review

Chickpea (Cicer arietinum L.) is an important grain legume that is grown and consumed all over the world. Chickpea is mostly grown in rainfed areas and marginal soils with low available zinc (Zn); however, its productivity is affected by micronutrient deficiencies in soil, particularly Zn deficiency. Zinc is a structural constituent and regulatory cofactor of enzymes involved in various plant biochemical pathways. As such, Zn deficiency impairs plant growth and development by reducing enzyme activity, disturbing ribosomal stabilisation, and decreasing the rate of protein synthesis. Moreover, Zn deficiency induces flower abortion and ovule infertility, leading to low seedset and substantial yield reductions. Nonetheless, inclusion of chickpea in cropping systems (e.g. rice–wheat), either in rotation or intercropped with cereals, improves Zn availability in the soil through the release of phosphatases, carboxylates, and protons by roots and soil microbes. This review discusses the role of Zn in chickpea biology, various factors affecting Zn availability, and Zn dynamics in soil and chickpea-based cropping systems. The review also covers innovative breeding strategies for developing Zn-efficient varieties, biofortification, and agronomic approaches for managing Zn deficiency in chickpea. Strategies to improve grain yield and grain Zn concentration in chickpea through use of different Zn-application methods—soil, foliar and seed treatments—that are simple, efficient and cost-effective for farmers are also discussed. Screening of efficient genotypes for root Zn uptake and translocation to the grain should be included in breeding programs to develop Zn-efficient chickpea genotypes.

Influences of carbohydrate, nitrogen, and phosphorus sources on the citric acid production by fungal endophyte Aspergillus fumigatus P3I6

Fungi are ecologically ubiquitous organisms on earth and regarded as one of the prolific sources of natural products. Fungal endophytes may provide essential prerequisite molecules to plant biochemical pathways which allow the efficient synthesis of primary and secondary metabolites. This study characterized the influences of various combinations of process parameters namely, carbohydrate, nitrogen, and phosphorus sources on citric acid (CA) production by the isolated fungal endophyte Aspergillus fumigatus P3I6 from Citrus microcarpa. Aspergillus fumigatus P3I6 had higher CA concentration of 9.2 (± 0.9) g L−1 and 9.0 (± 5.0 × 10−15) g L−1 when supplemented with sucrose and white refined sugar, respectively, than A. niger NRRL 599. Response Surface Methodology (RSM) had shown that A. fumigatus P3I6 produced the highest CA (23.8 g L−1) in Combination 4 (18.0% sucrose, 0.3 g L−1 ammonium sulfate, and 5.0 g L−1 dipotassium phosphate (K2HPO4)). Analysis of variance showed that when K2HPO4 concentrations were increased, CA content in fermentation media was significantly elevated. Hence, K2HPO4 was the most critical variable in the quadratic model (p < 0.05); however, sucrose concentration still has its role in production. Aside from using A. niger in most fermentation processes, this discovered fungal strain can be potentially used in biotechnological applications.

High-throughput field phenotyping using hyperspectral reflectance and partial least squares regression (PLSR) reveals genetic modifications to photosynthetic capacity

Spectroscopy is becoming an increasingly powerful tool to alleviate the challenges of traditional measurements of key plant traits at the leaf, canopy, and ecosystem scales. Spectroscopic methods often rely on statistical approaches to reduce data redundancy and enhance useful prediction of physiological traits. Given the mechanistic uncertainty of spectroscopic techniques, genetic modification of plant biochemical pathways may affect reflectance spectra causing predictive models to lose power. The objectives of this research were to assess over two separate years, whether a predictive model can represent natural and imposed variation in leaf photosynthetic potential for different crop cultivars and genetically modified plants, to assess the interannual capabilities of a partial least square regression (PLSR) model, and to determine whether leaf N is a dominant driver of photosynthesis in PLSR models. In 2016, a PLSR analysis of reflectance spectra coupled with gas exchange data was used to build predictive models for photosynthetic parameters including maximum carboxylation rate of Rubisco (Vc,max), maximum electron transport rate (Jmax) and percentage leaf nitrogen ([N]). The model was developed for wild type and genetically modified plants that represent a wide range of photosynthetic capacities. Results show that hyperspectral reflectance accurately predicted Vc,max, Jmax and [N] for all plants measured in 2016. Applying these PLSR models to plants grown in 2017 resulted in a strong predictive ability relative to gas exchange measurements for Vc,max, but not for Jmax, and not for genotypes unique to 2017. Building a new model including data collected in 2017 resulted in more robust predictions, with R2 increases of 17% for Vc,max. and 13% Jmax. Plants generally have a positive correlation between leaf nitrogen and photosynthesis, however, tobacco with reduced Rubisco (SSuD) had significantly higher [N] despite much lower Vc,max. The PLSR model was able to accurately predict both lower Vc,max and higher leaf [N] for this genotype suggesting that the spectral based estimates of Vc,max and leaf nitrogen [N] are independent. These results suggest that the PLSR model can be applied across years, but only to genotypes used to build the model and that the actual mechanism measured with the PLSR technique is not directly related to leaf [N]. The success of the leaf-scale analysis suggests that similar approaches may be successful at the canopy and ecosystem scales but to use these methods across years and between genotypes at any scale, application of accurately populated physical based models based on radiative transfer principles may be required.

Characterization of squalene-induced PgCYP736B involved in salt tolerance by modulating key genes of abscisic acid biosynthesis

Cytochrome P450 genes as the one of the largest superfamily genes mediate a wide range of plant biochemical pathways. In this study, a full-length cytochrome P450 monooxygenase (CYP736B) cDNA was isolated and characterized from Panax ginseng. It was revealed that the deduced amino acid of PgCYP736B shares a high degree of sequence homology with CYP736A12 encoded by P. ginseng. Expression of PgCYP736B was differentially induced not only during a Pseudomonas syringae infection (7.7-fold) and wounding (47.3-fold) but also after exposure to salt (7.4-fold), cold (8.3-fold), and drought stress (3.24-fold). The gene transcription was highly affected by methyl jasmonate (476-fold) in the ginseng, suggesting that PgCYP736B was elicitor-responsive. Furthermore, we overexpressed the PgCYP736B gene in Arabidopsis and found that PgCYP736B is a transmembrane protein. Overexpression of PgCYP736B in Arabidopsis conferred enhanced resistance to salt stress via decreased H2O2 accumulation, increased carotenoid levels, and through abscisic acid biosynthesis gene expression. Our results suggest that the induction of ginsenoside biosynthetic pathway genes along with PgCYP736B by an exogenous supply of 10–100 μM of squalene most likely affects the metabolite profile of ginsenoside triterpenoid. Overall, our findings indicate that PgCYP736B protects ginseng from salt stress and may contribute to triterpenoid biosynthesis.

Several Pesticides Influence the Nutritional Content of Sweet Corn.

Herbicides are pesticides used to eradicate unwanted plants in both crop and non-crop environments. These chemistries are toxic to weeds due to inhibition of key enzymes or disruption of essential biochemical processes required for weedy plants to survive. Crops can survive systemic herbicidal applications through various forms of detoxification, including metabolism that can be enhanced by safeners. Field studies were conducted near Louisville, Tennessee and Painter, Virginia to determine how the herbicides mesotrione, topramezone, nicosulfuron, and atrazine applied with or without the safener isoxadifen-ethyl would impact the nutritional quality of "Incredible" sweet corn ( Zea mays L. var. rugosa). Several herbicide treatments increased the uptake of the mineral elements phosphorus, magnesium, and manganese by 8-75%. All herbicide treatments increased protein content by 4-12%. Applied alone, nicosulfuron produced similar levels of saturated, monounsaturated, and polyunsaturated fatty acids when compared to the nontreated check, but when applied with isoxadifen-ethyl, fatty acids increased 8 to 44% relative to the check or control. Nicosulfuron plus isoxadifen-ethyl or topramezone or the combination of all three actives increased the concentrations of fructose and glucose (40-68%), whereas reducing levels of maltose or sucrose when compared to the nontreated check (-15 to -21%). Disruptions in biochemical pathways in plants due to the application of herbicides, safeners, or other pesticides have the potential to alter the nutrient quality, taste, and overall plant health associated with edible crops.

ROLE OF IRON IN PLANT GROWTH AND METABOLISM

Iron is an essential micronutrient for almost all living organisms because of it plays critical role in metabolic processes such as DNA synthesis, respiration, and photosynthesis. Further, many metabolic pathways are activated by iron, and it is a prosthetic group constituent of many enzymes. An imbalance between the solubility of iron in soil and the demand for iron by the plant are the primary causes of iron chlorosis. Although abundant in most well-aerated soils, the biological activity of iron is low because it primarily forms highly insoluble ferric compounds at neutral pH levels. Iron plays a significant role in various physiological and biochemical pathways in plants. It serves as a component of many vital enzymes such as cytochromes of the electron transport chain, and it is thus required for a wide range of biological functions. In plants, iron is involved in the synthesis of chlorophyll, and it is essential for the maintenance of chloroplast structure and function. There are seven transgenic approaches and combinations, which can be used to increase the concentration of iron in rice seeds. The first approach involves enhancing iron accumulation in rice seeds by expressing the ferritin gene under the control of endosperm-specific promoters. The second approach is to increase iron concentrations in rice through overexpression of the nicotianamine synthase gene (NAS). Nicotianamine, which is a chelator of metal cations, such as Fe+2 and zinc (Zn+2), is biosynthesized from methionine via S-adenosyl methionine synthase. The third approach is to increase iron concentrations in rice and to enhance iron influx to seeds by expressing the Fe+2- nicotianamine transporter gene OsYSL2. The fourth approach to iron biofortification involves enhancing iron uptake and translocation by introducing genes responsible for biosynthesis of mugineic acid family phytosiderophores (MAs). The fifth approach to enhance iron uptake from soil is the over expression of the OsIRT1 or OsYSL15 iron transporter genes. The sixth approach to enhanced iron uptake and translocation is overexpression of the iron homeostasis-related transcription factor OsIRO2. OsIRO2 is responsible for the regulation of key genes involved in MAs-related iron uptake. The seventh approach to enhanced iron translocation from flag leaves to seeds utilizes the knockdown of the vacuolar iron transporter gene OsVIT1 or OsVIT2. The present review discusses iron toxicity in plants with regard to plant growth and metabolism, metal interaction, iron-acquisition mechanisms, biofortification of iron, plant-iron homeostasis, gene function in crop improvement, and micronutrient interactions.

SELENIUM FERTILIZATION INFLUENCES BIOMASS, ELEMENTAL ACCUMULATIONS, AND PHYTOCHEMICAL CONCENTRATIONS IN WATERCRESS

Watercress (Nasturtium officinale R. Br.) produces carotenoids and sulfur-containing glucosinolates (GSs) beneficial to human health. Selenium (Se) imparts dietary health properties and substitutes for S in plant biochemical pathways. Experimental objectives were to determine the influence of Se fertilization on 1) biomass, 2) elemental accumulations, 3) carotenoids, and 4) glucosinolates in watercress leaf and shoot tissues. Watercress was greenhouse grown in solution culture with Se treatments of 0, 0.125, 0.25, 0.50, 1.0, 2.0, and 4.0 mg Se L−1, delivered as sodium selenate (Na2SeO4). Fresh and dry biomass were unaffected while shoot tissue Se (P = 0.057) and S (P = 0.003) increased linearly in response to increasing Se treatments. Linear decreases were measured for β-carotene (P = 0.017) and lutein (P = 0.018) in response to increasing Se. Total levels of GS increased, then decreased quadratically (P = 0.003). Results indicate that Se supplementation can increase Se tissue concentrations and GS in watercress; however, carotenoids were negatively affected.

Plant Protein Kinase and Protein-Protein Interaction

External and internal stimuli trigger the response of signals in the cell which amplified and communicated by various complex signal transduction networks are mostly initiated with the activation of different receptor proteins. These signaling networks perform as protective strategy to allow cells to cope with external stresses that usually restrain the plant growth and development. Protein kinases are among the most common cellular regulatory components of signal transduction in plants. Protein phosphorylation plays prominent role in various biochemical pathways in plants as a result of active implication in the regulation of cell growth and development. Therefore, protein kinase becomes the most common target used to improve plant growth and development. Gravity force, touch, light, gradients in temperature, humidity, ions, chemicals and oxygen are among the environmental elements influencing the physiological and biological aspects of plants. Hence, many different plant species adopt and response to different environmental stresses where they develop physiological strategies to generate their optimum growth. Beside the involvement in the signal transduction pathways, protein kinases also encourage the proteinprotein interaction events within the cells. Therefore, protein phosphorylation plays pivotal roles in activating the protein kinases and transcription factors in various signal transduction pathways. A process whereby a cell communicates and responses to the stimuli from external environment to alter its growth, development, physiology and morphology is known as signal transduction. This signal transduction process involves a serial of biochemical phenomenon that are performed and conducted by many types of enzymes within the cells. Most of the signals are perceived and recognized at the cell surface. The integration and interaction of various signaling information and activities are important, for example, addition of a phosphate to a protein kinase to target the protein substrate. Hence, modification of protein forms protein-protein interaction useful for signal transduction in plant growth and development.

English

Bioregulators are chemicals that affect the expression of biological responses in plant tissues. Their use is a unique facet of biotechnology and a new approach of manipulating plant biochemistry for enhancing productivity and quality. They act in low concentrations without any biocidal or nutritive action. Applications of bioregulators are reported to reduce biotic and abiotic stress in plants. Recent studies show that their application increases the growth, yield and nutritive value of food crops. Their use at different times or concentrations elicits diverse effects and in some cases significantly alters virus multiplication and pathogenesis. Increasingly, plant bioregulators are being recognised as important tools in pest and disease management. They have been instrumental in understanding morphological and growth phenomena in-vitro and are potential tools for elucidating biochemical pathways in plants. Plant growth and development are influenced by physical, chemical and biological components in the plants’ environment. Though, bioregulators are commonly used to improve plant growth, development, defence and productivity, the molecular mechanisms of their effects still remain to be fully elucidated. This article reviews the biochemical importance of bioregulator application in plants, current state of research on their effects and discusses their roles in insect and pest invasion as well as possible mechanism of action. Key words: Bioregulation, plant growth, plant development, plant improvement, stresses

De Novo Transcriptome Sequencing in Trigonella foenum‐graecum L. to Identify Genes Involved in the Biosynthesis of Diosgenin

Trigonella foenum‐graecum L. (fenugreek) is a viable alternative for production of diosgenin because of its shorter growing cycle, lower production costs, and consistent yield and quality. We studied de novo transcriptome analysis along with the diosgenin pathway in Trigonella foenum‐graecum and identified the genes responsible for diosgenin biosynthesis. The GMV‐1 variety of Trigonella foenum‐graecum has been used in the present study for transcriptome analysis by sequencing messenger ribonucleic acid (RNA) with a SOLiD 4 Genome Analyzer. Deep sequencing data of the transcriptome was assembled using various assembly tools along with functional annotation of genes, and pathway analysis for diosgenin biosynthesis was deciphered. A total of 42 million high quality reads were obtained. De novo assembly was performed using Velvet at different k‐mer, Oases, and CLC Genomics Workbench, which generated 20,561 transcript contigs. CAP3 was used to reduce the redundancy of contigs obtained through these assemblers. A total of 18,333 transcript contigs were functionally annotated. Kyoto Encyclopedia of Genes and Genomes pathway mapping showed that 6775 transcripts were related to plant biochemical pathways including the diosgenin biosynthesis pathway. The large number of transcripts reported in the current study will serve as a valuable genetic resource for Trigonella foenum‐graecum. Sequence information of the genes that were involved in diosgenin biosynthesis could be used for metabolic engineering of Trigonella foenum‐graecum to increase diosgenin content.

Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence

Plant natural product research can be facilitated through genome and transcriptome sequencing approaches that generate informative sequence and expression datasets that enable characterization of biochemical pathways of interest. As the overwhelming majority of plant-derived natural products are derived from species with little, if any, sequence and/or genomic resources, the ability to perform whole genome shotgun sequencing and assembly has been and will continue to be transformative as access to a genome sequence provides molecular resources and a context for discovery and characterization of biosynthetic pathways. Due to the reduced size and complexity of the transcriptome relative to the genome, transcriptome sequencing provides a rapid, inexpensive approach to access gene sequences, gene expression abundances, and gene expression patterns in any species, including those that lack a reference genome sequence. To date, successful applications of RNA sequencing in conjunction with de novo transcriptome assembly has enabled identification of new genes in an array of biochemical pathways in plants. While sequencing technologies are well developed, challenges remain in the handling and analysis of transcriptome sequences. In this Highlight article, we provide an overview of the bioinformatics challenges associated with transcriptome analyses using short read sequences and how to address these issues in plant species that lack a reference genome.

Microbially Mediated Plant Functional Traits

Plants are rife with bacteria and fungi that colonize roots and shoots both externally and internally. By providing novel nutritional and defense pathways and influencing plant biochemical pathways, microbes can fundamentally alter plant phenotypes. Here we review the widespread nature of microbially mediated plant functional traits. We highlight that there is likely fitness conflict between hosts and symbionts and that fitness outcomes can depend on partner genotypes and ecological factors. Microbes may influence ecosystems through their effects on the functional trait values and population dynamics of their plant hosts. These effects may feed back on symbiont evolution by altering transmission rates of symbionts and scale up to ecosystem processes and services. We end by proposing new avenues of research in this emerging field.

Korean plant proteomics: pioneers in plant stress physiology

Abstract Plant proteomics is the large-scale studies of proteins, particularly on their structures and functions, governed by the physiological metabolism of plant cells. With the development of techniques and strategies in pro-teomics, proteomics approach is moving forward in systems biology handling sophisticated components of major signaling and biochemical pathways in plants responding to their environment. In Korea, pioneers in plant proteomics are trying to catch up with global trends in plant proteomics; these researchers are not only improving existing techniques in protein extraction but also developing new techniques in proteomics context. In the hot field of abiotic and biotic stress proteomics, 29 and 9 out of 74 papers have been published during the review period from 2005 to 2010, respectively. This present review article provides an overview on the output of Korean plant proteomers while paying special attention to both abiotic and biotic stress proteomics. Keywords South Korea, Plant, Proteomics, Abiotic, Biotic, Stress Physiology