Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation

Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria

Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. Saponaria vaccaria is an annual herb used in traditional Chinese medicine, containing large quantities of oleanane-type triterpenoid saponins with anticancer properties and structural similarities to the vaccine adjuvant QS-21. Leveraging the MeJA-elicited saponin biosynthesis, we identify multiple enzymes catalyzing the oxidation and glycosylation of triterpenoids in S. vaccaria. This exploration is aided by Pacbio full-length transcriptome sequencing and gene expression analysis. A cellulose synthase-like enzyme can not only glucuronidate triterpenoid aglycones but also alter the product profile of a cytochrome P450 monooxygenase via preference for the aldehyde intermediate. Furthermore, the discovery of a UDP-glucose 4,6-dehydratase and a UDP-4-keto-6-deoxy-glucose reductase reveals the biosynthetic pathway for the rare nucleotide sugar UDP-D-fucose, a likely sugar donor for fucosylation of plant natural products. Our work enables the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.

Methyl jasmonate-induced senescence results in alterations in the status of chlorophyll precursors and enzymatic antioxidants in rice plants

We examined the control of chlorophyll biosynthesis and protective mechanisms during leaf senescence induced by methyl jasmonate (MeJA). After MeJA treatment, rice plants displayed evidence of great oxidative stress regarding senescence symptoms, disruption of membrane integrity, H₂O₂ production, and decreased chlorophyll content and photosynthetic efficiency. After 6 h of MeJA treatment, plants greatly decreased not only their levels of chlorophyll precursors, including protoporphyrin IX (Proto IX), Mg-Proto IX, Mg-Proto IX methylester, and protochlorophyllide, but also the expression levels of the chlorophyll biosynthetic genes CHLD, CHLH, CHLI, and PORB, with the greatest decreases at 78 h. MeJA-treated plants showed a noticeable degradation of light-harvesting chlorophyll-binding proteins (LHCB) at 78 h after MeJA treatment but began to downregulate expression of LHCB at 6 h. Photoprotection, as indicated by nonphotochemical quenching, slightly increased only at 6 h after MeJA treatment. In parallel to the increased activities of superoxide dismutase, catalase (CAT), ascorbate peroxidase (APX), and peroxidase, MeJA-treated plants responded to senescence by markedly upregulating the expression of APX and CAT. Our study demonstrates that rice plants developed protective mechanisms for mitigating oxidative stress by scavenging phototoxic chlorophyll precursors and activating enzymatic antioxidant responses during MeJA-induced senescence.

GlPS1 overexpression accumulates coumarin secondary metabolites in transgenic Arabidopsis

The dried root of Glehnia littoralis is a traditional Chinese herbal medicine mainly used to treat lung diseases and plays an important role in fighting coronavirus disease 2019 pneumonia in China. This study focused on the key enzyme gene GlPS1 for furanocoumarin synthesis in G. littoralis. In the 35S:GlPS1 transgenic Arabidopsis study, the Arabidopsis thaliana-overexpressing GlPS1 gene was more salt-tolerant than Arabidopsis in the blank group. Metabolomics analysis showed 30 differential metabolites in Arabidopsis, which overexpressed the GlPS1 gene. Twelve coumarin compounds were significantly upregulated, and six of these coumarin compounds were not detected in the blank group. Among these differential coumarin metabolites, isopimpinellin and aesculetin have been annotated by the Kyoto Encyclopedia of Genes and Genomes and isopimpinellin was not detected in the blank group. Through structural comparison, imperatorin was formed by dehydration and condensation of zanthotoxol and a molecule of isoprenol, and the difference between them was only one isoprene. Results showed that the GlPS1 gene positively regulated the synthesis of coumarin metabolites in A. thaliana and at the same time improved the salt tolerance of A. thaliana.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11240-022-02427-w.

Linum lewisii Adventitious and Hairy-Roots Cultures as Lignan Plant Factories

Plants synthesize specific secondary metabolites for survival, reproduction, environmental resilience, and defense. Among them, lignans are a class of polyphenols with several bioactive properties: chemopreventive, anti-inflammatory, antiviral, and antioxidant. These compounds are often extracted from field-grown plants with very low yields. To overcome these constraints, in vitro tissue cultures provide a tool to optimize large-scale production. Moreover, the use of elicitation to increase secondary metabolite production is gaining importance. The aim of this work was to develop adventitious (ARL) and hairy roots (HRL) from Linum lewisi, a species able to synthesize arylnaphthalene lignans such as justicidin B. The ARL and HRL were obtained for the first time and characterized for their phenol content, antioxidant activity, and the production of justicidin B after treatments with several elicitors and precursor feeding. Through NMR spectroscopy, other four lignans were highlighted and identified in the roots extracts. A pilot-scale bioreactor was adopted to assess the suitability of the developed root cultures for future large-scale production. The ARL and HRL cultures showed a justicidin B production higher than other Linum species cultures described up to now (75.8 mg/L and 82.2 g/L), and the production more than doubled after elicitation with MeJA.

Volatile-mediated plant-plant interactions: volatile organic compounds as modulators of receiver plant defence, growth, and reproduction

It is firmly established that plants respond to biotic and abiotic stimuli by emitting volatile organic compounds (VOCs). These VOCs provide information on the physiological status of the emitter plant and are available for detection by the whole community. In the context of plant-plant interactions, research has focused mostly on the defence-related responses of receiver plants. However, responses may span hormone signalling and both primary and secondary metabolism, and ultimately affect plant fitness. Here we present a synthesis of plant-plant interactions, focusing on the effects of VOC exposure on receiver plants. An overview of the important chemical cues, the uptake and conversion of VOCs, and the adsorption of VOCs to plant surfaces is presented. This is followed by a review of the substantial VOC-induced changes to receiver plants affecting both primary and secondary metabolism and influencing plant growth and reproduction. Further research should consider whole-plant responses for the effective evaluation of the mechanisms and fitness consequences of exposure of the receiver plant to VOCs.

Effects of Preharvest Methyl Jasmonate and Salicylic Acid Treatments on Growth, Quality, Volatile Components, and Antioxidant Systems of Chinese Chives

Methyl jasmonate (MeJA) and salicylic acid (SA) regulate the production of biologically active compounds in plants and stimulate the accumulation of plant aromatic substances. However, the underlying mechanisms of how MeJA and SA influence characteristic flavor compounds and the antioxidant activity of vegetables are poorly understood. Five MeJA and SA concentrations were used to investigate the dose-dependent effects of these phytohormones on the dry and fresh weight; chlorophyll abundance; the contents of vitamin C, soluble protein, and sugar, nitrate, total phenols, flavonoids, volatile components, and enzymatically produced pyruvic acid; and antioxidant activity in Chinese chive. We found that MeJA and SA at concentrations of 500 and 150 μM, respectively, significantly increased the levels of total chlorophyll, phenols and flavonoids, vitamin C, and volatile components and significantly reduced the accumulation of nitrate. In addition, compared with the control, 500 μM of MeJA significantly increased the soluble sugar and protein content, and 150 μM SA significantly increased the dry and fresh weight of Chinese chive. Furthermore, these concentrations of MeJA and SA significantly increased the enzymatic pyruvate content and the amount of sulfide and aromatic volatile compounds and improved the characteristic flavor compounds. The 2,2-diphenyl-1-picrylhydrazyl radical scavenging capacity, Trolox-equivalent antioxidant capacity, and ferric-reducing antioxidant capacity were significantly improved after a preharvest treatment with 500 μM MeJA and 150 μM SA, which could improve the antioxidant activity, thus improving the postharvest quality and preservation characteristics of Chinese chives. Taken together, a preharvest treatment with 500 μM MeJA and 150 μM SA is optimal to improve the growth, quality, antioxidant activity, and flavor of Chinese chive, thereby enhancing its commercial value.

Biotechnological approaches to the production of plant-derived promising anticancer agents: An update and overview

The plant kingdom is a rich source of bioactive compounds, many of which have been used since pre-history for their therapeutic properties to treat a range of illnesses. These metabolites have recently attracted attention to their antineoplastic activities to treat various cancers relying on different mechanisms. Some of these molecules are glycosides, which have proven useful as anti-cancer agents, namely podophyllotoxin (PPT) anaryltetralin lignan or alkaloids. There are three primary forms of alkaloids, such as indole alkaloids (vincristine and vinblastine from Catharanthus roseus), quinoline alkaloid (camptothecin from Camptotheca acuminata), and diterpenoid alkaloid (taxol and it's analogous from Taxus and Corylus species). This review considers various plant biotechnology approaches used to enhance the production of these anticancer molecules in different species. In this regard, many in vitro culture techniques such as stimulation of suspension culture and hairy roots are being used to investigate the effects of plant growth regulators and elicitors on various explants.

Effects of exogenous methyl jasmonate on the synthesis of endogenous jasmonates and the regulation of photosynthesis in citrus

Methyl jasmonate (MeJA) is an airborne signaling phytohormone that can induce changes in endogenous jasmonates (JAs) and cause photosynthetic responses. However, the response of these two aspects of citrus plants at different MeJA concentrations is still unclear. Four MeJA concentrations were used in two citrus varieties, Huangguogan (C. reticulata × C. sinensis) and Shiranuhi [C. reticulata × (C. reticulata × C. sinensis)], to investigate the effects of MeJA dose on the endogenous JAs pathway and photosynthetic capacity. We observed that MeJA acted in a dose-dependent manner, and its stimulation in citrus leaves showed a bidirectional character at different concentrations. This work demonstrates that MeJA at only a concentration of 2.2 mM or less contributed to the activation of magnesium protoporphyrin IX methyltransferase (ChlM, EC 2.1.1.11) and protochlorophyllide oxidoreductase (POR, EC 1.3.1.11) and the simultaneous accumulation of Chl a and Chl b, which in turn contributed to an improved photosynthetic capacity and PSII photochemistry efficiency of citrus. Meanwhile, the inhibition of endogenous JAs synthesis by exogenous MeJA was observed. This was achieved by reducing the ratio of monogalactosyl diacylglycerol (MGDG) to diagalactosyl diacylglycerol (DGDG) and inhibiting the activities of key enzymes in JAs synthesis, especially 12-oxo-phytodienoic acid reductase (OPR, EC 1.3.1.42). Another noteworthy finding is that there may exist a JA-independent pathway that could regulate 12-oxo-phytodienoic acid (OPDA) synthesis. This study jointly analyzed the internal hormone regulation mechanism and the external physiological response, as well as revealed the effects of exogenous MeJA on promoting the photosynthesis and inhibiting the endogenous JAs synthesis.

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.

De novo transcriptome analysis unravels tissue-specific expression of candidate genes involved in major secondary metabolite biosynthetic pathways of Plumbago zeylanica: implication for pharmacological potential

KEY MESSAGE

The present study provides comparative transcriptome analysis, besides identifying functional secondary metabolite genes of Plumbago zeylanica with pharmacological potential for future functional genomics, and metabolomic engineering of secondary metabolites from this plant towards diversified biomedical applications.

ABSTRACT

Plumbago zeylanica is a widely used medicinal plant of the traditional Indian system of medicine with wide pharmacological potential to treat several disorders. The present study aimed to carry out comparative transcriptome analysis in leaf and root tissue of P. zeylanica using Illumina paired end sequencing to identify tissue-specific functional genes involved in the biosynthesis of secondary metabolites, contributing to its therapeutic efficacy. De novo sequencing assembly resulted in the identification of 62,321 "Unigenes" transcripts with an average size of 1325 bp. Functional annotation using BLAST2GO resulted in the identification of 50,301 annotated transcripts (80.71%) and GO assigned to 18,814 transcripts. KEGG pathway annotation of the "Unigenes" revealed that 2465 transcripts could be assigned to 242 KEGG pathway maps wherein the number of transcripts involved in secondary metabolism was distinct in root and leaf transcriptome. Among the secondary metabolite biosynthesis pathways, the cluster of "Unigenes" encoding enzymes of 'Phenylpropanoid biosynthesis pathway' represents the largest group (84 transcripts) followed by 'Terpenoid Backbone biosynthesis' (48 transcripts). The transcript levels of the candidate unigenes encoding key enzymes of phenylpropanoid (PAL, TAL) and flavanoid biosynthesis (CHS, ANS, FLS) pathways were up-regulated in root, while the expression levels of candidate "Unigenes" transcript for monoterpenoid (DXS, ISPF), diterpenoid biosynthesis (SPS, SDS) and indole alkaloid pathways (STR) were significantly higher in leaf of P. zeylanica. Interestingly, validation of differential gene expression profile by qRT-PCR also confirmed that candidate "Unigenes" enzymes of phenylpropanoid and flavonoid biosynthesis were highly expressed in the root, while the key regulatory enzymes of terpenoid and indole alkaloid compounds were up-regulated in the leaf, suggesting that (differences in) the levels of these functional genes could be attributed to the (differential) pharmacological activity (between root and leaf) in tissues of P. zeylanica.

Transcriptome-wide shift from photosynthesis and energy metabolism upon endogenous fluid protein depletion in young Nepenthes ampullaria pitchers

Carnivorous pitcher plants produce specialised pitcher organs containing secretory glands, which secrete acidic fluids with hydrolytic enzymes for prey digestion and nutrient absorption. The content of pitcher fluids has been the focus of many fluid protein profiling studies. These studies suggest an evolutionary convergence of a conserved group of similar enzymes in diverse families of pitcher plants. A recent study showed that endogenous proteins were replenished in the pitcher fluid, which indicates a feedback mechanism in protein secretion. This poses an interesting question on the physiological effect of plant protein loss. However, there is no study to date that describes the pitcher response to endogenous protein depletion. To address this gap of knowledge, we previously performed a comparative RNA-sequencing experiment of newly opened pitchers (D0) against pitchers after 3 days of opening (D3C) and pitchers with filtered endogenous proteins (>10 kDa) upon pitcher opening (D3L). Nepenthes ampullaria was chosen as a model study species due to their abundance and unique feeding behaviour on leaf litters. The analysis of unigenes with top 1% abundance found protein translation and stress response to be overrepresented in D0, compared to cell wall related, transport, and signalling for D3L. Differentially expressed gene (DEG) analysis identified DEGs with functional enrichment in protein regulation, secondary metabolism, intracellular trafficking, secretion, and vesicular transport. The transcriptomic landscape of the pitcher dramatically shifted towards intracellular transport and defence response at the expense of energy metabolism and photosynthesis upon endogenous protein depletion. This is supported by secretome, transportome, and transcription factor analysis with RT-qPCR validation based on independent samples. This study provides the first glimpse into the molecular responses of pitchers to protein loss with implications to future cost/benefit analysis of carnivorous pitcher plant energetics and resource allocation for adaptation in stochastic environments.

Methyl jasmonate-induced compositional changes of volatile organic compounds in Polygonum minus leaves

Polygonum minus Huds. is a medicinal aromatic plant rich in terpenes, aldehydes, and phenolic compounds. Methyl jasmonate (MeJA) is a plant signaling molecule commonly applied to elicit stress responses to produce plant secondary metabolites. In this study, the effects of exogenous MeJA treatment on the composition of volatile organic compounds (VOCs) in P. minus leaves were investigated by using a metabolomic approach. Time-course changes in the leaf composition of VOCs on days 1, 3, and 5 after MeJA treatment were analyzed through solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). The VOCs found in MeJA-elicited leaves were similar to those found in mock-treated leaves but varied in quantity at different time points. We focused our analysis on the content and composition of monoterpenes, sesquiterpenes, and green leaf volatiles (GLVs) within the leaf samples. Our results suggest that MeJA enhances the activity of biosynthetic pathways for aldehydes and terpenes in P. minus. Hence, the production of aromatic compounds in this medicinal herb can be increased by MeJA elicitation. Furthermore, the relationship between MeJA elicitation and terpene biosynthesis in P. minus was shown through SPME-GC-MS analysis of VOCs combined with transcriptomic analysis of MeJA-elicited P. minus leaves from our previous study.

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Background

Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food industries. Although the terpenoids of P. minor have been studied thoroughly, the involvement of microRNA (miRNA) in terpenoid regulation remains poorly understood and needs to be explored. In this study, P. minor plants were inoculated with the pathogenic fungus Fusarium oxysporum for terpenoid induction.

Result

SPME GC-MS analysis showed the highest terpenoid accumulation on the 6th day post-inoculation (dpi) compared to the other treatment time points (0 dpi, 3 dpi, and 9 dpi). Among the increased terpenoid compounds, α-cedrene, valencene and β-bisabolene were prominent. P. minor inoculated for 6 days was selected for miRNA library construction using next generation sequencing. Differential gene expression analysis showed that 58 miRNAs belonging to 30 families had significantly altered regulation. Among these 58 differentially expressed genes (DEGs), 33 miRNAs were upregulated, whereas 25 miRNAs were downregulated. Two putative novel pre-miRNAs were identified and validated through reverse transcriptase PCR. Prediction of target transcripts potentially involved in the mevalonate pathway (MVA) was carried out by psRobot software, resulting in four miRNAs: pmi-miR530, pmi-miR6173, pmi-miR6300 and a novel miRNA, pmi-Nov_13. In addition, two miRNAs, miR396a and miR398f/g, were predicted to have their target transcripts in the non-mevalonate pathway (MEP). In addition, a novel miRNA, pmi-Nov_12, was identified to have a target gene involved in green leaf volatile (GLV) biosynthesis. RT-qPCR analysis showed that pmi-miR6173, pmi-miR6300 and pmi-nov_13 were downregulated, while miR396a and miR398f/g were upregulated. Pmi-miR530 showed upregulation at 9 dpi, and dynamic expression was observed for pmi-nov_12. Pmi-6300 and pmi-miR396a cleavage sites were detected through degradome sequence analysis. Furthermore, the relationship between miRNA metabolites and mRNA metabolites was validated using correlation analysis.

Conclusion

Our findings suggest that six studied miRNAs post-transcriptionally regulate terpenoid biosynthesis in P. minor. This regulatory behaviour of miRNAs has potential as a genetic tool to regulate terpenoid biosynthesis in P. minor.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5954-0) contains supplementary material, which is available to authorized users.

Comparative transcriptome analyses revealed differential strategies of roots and leaves from methyl jasmonate treatment Baphicacanthus cusia (Nees) Bremek and differentially expressed genes involved in tryptophan biosynthesis

Baphicacanthus cusia (Nees) Bremek (B. cusia) is an effective herb for the treatment of acute promyelocytic leukemia and psoriasis in traditional Chinese medicine. Methyl jasmonate (MeJA) is a well-known signaling phytohormone that triggers gene expression in secondary metabolism. Currently, MeJA-mediated biosynthesis of indigo and indirubin in B. cusia is not well understood. In this study, we analyzed the content of indigo and indirubin in leaf and root tissues of B. cusia with high-performance liquid chromatography and measured photosynthetic characteristics of leaves treated by MeJA using FluorCam6 Fluorometer and chlorophyll fluorescence using the portable photosynthesis system CIRAS-2. We performed de novo RNA-seq of B. cusia leaf and root transcriptional profiles to investigate differentially expressed genes (DEGs) in response to exogenous MeJA application. The amount of indigo in MeJA-treated leaves were higher than that in controled leaves (p = 0.004), and the amounts of indigo in treated roots was higher than that in controlled roots (p = 0.048); Chlorophyll fluorescence of leaves treated with MeJA were significantly decreased. Leaves treated with MeJA showed lower photosynthetic rate compared to the control in the absence of MeJA. Functional annotation of DEGs showed the DEGs related to growth and development processes were down-regulated in the treated leaves, while most of the unigenes involved in the defense response were up-regulated in treated roots. This coincided with the effects of MeJA on photosynthetic characteristics and chlorophyll fluorescence. The qRT-PCR results showed that MeJA appears to down-regulate the gene expression of tryptophan synthase β-subunits (trpA-β) in leaves but increased the gene expression of anthranilate synthase (trp 3) in roots responsible for increased indigo content. The results showed that MeJA suppressed leaf photosynthesis for B. cusia and this growth-defense trade-off may contribute to the improved adaptability of B. cusia in changing environments.

Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation

BACKGROUND

Jasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, Persicaria minor, which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like P. minor is unknown.

METHOD

In this study, P. minor plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression.

RESULTS

From this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson's r = 0.677) while a weak correlation was observed for downregulated proteins (r = 0.147).

DISCUSSION

MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak (r = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.

Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content

Sugarcane (Saccharum spp. hybrids) is a potential lignocellulosic feedstock for biofuel production due to its exceptional biomass accumulation ability, high convertible carbohydrate content and a favorable energy input/output ratio. Genetic modification of biofuel traits to improve biomass conversion requires an understanding of the regulation of carbohydrate and lignin biosynthesis. RNA-Seq was used to investigate the transcripts differentially expressed between the immature and mature tissues of the sugarcane genotypes varying in fiber content. Most of the differentially expressed transcripts were found to be down-regulated during stem maturation, highlighting their roles in active secondary cell-wall development in the younger tissues of both high and low fiber genotypes. Several cellulose synthase genes (including CesA2, CesA4, CesA7 and COBRA-like protein), lignin biosynthesis-related genes (ρ-coumarate 3-hydroxylase, ferulate 5-hydroxylase, cinnamyl alcohol dehydrogenase and gentiobiase) and transcription regulators for the secondary cell-wall synthesis (including LIM, MYB, PLATZ, IAA24, C2H2 and C2C2 DOF zinc finger gene families) were exclusively differentially expressed between immature and mature tissues of high fiber genotypes. These findings reveal target genes for subsequent research on the regulation of cellulose and lignin metabolism.

Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome

In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant, Persicaria minor (P. minor) using computational approach. Unannotated sequences from deep sequencing were analyzed based on previous well-established parameters. Around 24 putative novel miRNAs were identified from 6,417,780 reads of the unannotated sequence which represented 11 unique putative miRNA sequences. PsRobot target prediction tool was deployed to identify the target transcripts of putative novel miRNAs. Most of the predicted target transcripts (mRNAs) were known to be involved in plant development and stress responses. Gene ontology showed that majority of the putative novel miRNA targets involved in cellular component (69.07%), followed by molecular function (30.08%) and biological process (0.85%). Out of 11 unique putative miRNAs, 7 miRNAs were validated through semi-quantitative PCR. These novel miRNAs discoveries in P. minor may develop and update the current public miRNA database.

Extensive mass spectrometry proteomics data of Persicaria minor herb upon methyl jasmonate treatment

Proteomics is often hindered by the lack of protein sequence database particularly for non-model species such as Persicaria minor herbs. An integrative approach called proteomics informed by transcriptomics is possible [1], in which translated transcriptome sequence database is used as the protein sequence database. In this current study, the proteome profile were profiled using SWATH-MS technology complemented with documented transcriptome profiling [2], the first such report in this tropical herb. The plant was also elicited using a phytohormone, methyl jasmonate (MeJA) and protein changes were elucidated using label-free quantification of SWATH-MS to understand the role of such signal molecule in this herbal species. The mass spectrometry proteomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD005749. This data article refers to the article entitled "Proteomics (SWATH-MS)-informed by transcriptomics approach of Persicaria minor leaves upon methyl jasmonate elicitation" [3].

Functional Genomics

Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.

Comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri identifies potential genes related to triterpenoid saponin biosynthesis

Background

Bacopa monnieri commonly known as Brahmi is utilized in Ayurveda to improve memory and many other human health benefits. Bacosides enriched standardized extract of Bacopa monnieri is being marketed as a memory enhancing agent. In spite of its well known pharmacological properties it is not much studied in terms of transcripts involved in biosynthetic pathway and its regulation that controls the secondary metabolic pathway in this plant. The aim of this study was to identify the potential transcripts and provide a framework of identified transcripts involved in bacosides production through transcriptome assembly.

Results

We performed comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri in two independent biological replicate and obtained 22.48 million and 22.0 million high quality processed reads in shoot and root respectively. After de novo assembly and quantitative assessment total 26,412 genes got annotated in root and 18,500 genes annotated in shoot sample. Quality of raw reads was determined by using SeqQC-V2.2. Assembled sequences were annotated using BLASTX against public database such as NR or UniProt. Searching against the KEGG pathway database indicated that 37,918 unigenes from root and 35,130 unigenes from shoot were mapped to 133 KEGG pathways. Based on the DGE data we found that most of the transcript related to CYP450s and UDP-glucosyltransferases were specifically upregulated in shoot tissue as compared to root tissue. Finally, we have selected 43 transcripts related to secondary metabolism including transcription factor families which are differentially expressed in shoot and root tissues were validated by qRT-PCR and their expression level were monitored after MeJA treatment and wounding for 1, 3 and 5 h.

Conclusions

This study not only represents the first de novo transcriptome analysis of Bacopa monnieri but also provides information about the identification, expression and differential tissues specific distribution of transcripts related to triterpenoid sapogenin which is one of the most important pharmacologically active secondary metabolite present in Bacopa monnieri. The identified transcripts in this study will establish a foundation for future studies related to carrying out the metabolic engineering for increasing the bacosides biosynthesis and its regulation for human health benefits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3865-5) contains supplementary material, which is available to authorized users.