Divergent Roles of the Auxin Response Factors in Lemongrass (Cymbopogon flexuosus (Nees ex Steud.) W. Watson) during Plant Growth.

Auxin Response Factors (ARFs) make up a plant-specific transcription factor family that mainly couples perception of the phytohormone, auxin, and gene expression programs and plays an important and multi-faceted role during plant growth and development. Lemongrass (Cymbopogon flexuosus) is a representative Cymbopogon species widely used in gardening, beverages, fragrances, traditional medicine, and heavy metal phytoremediation. Biomass yield is an important trait for several agro-economic purposes of lemongrass, such as landscaping, essential oil production, and phytoremediation. Therefore, we performed gene mining of CfARFs and identified 26 and 27 CfARF-encoding genes in each of the haplotype genomes of lemongrass, respectively. Phylogenetic and domain architecture analyses showed that CfARFs can be divided into four groups, among which groups 1, 2, and 3 correspond to activator, repressor, and ETTN-like ARFs, respectively. To identify the CfARFs that may play major roles during the growth of lemongrass plants, RNA-seq was performed on three tissues (leaf, stem, and root) and four developmental stages (3-leaf, 4-leaf, 5-leaf. and mature stages). The expression profiling of CfARFs identified several highly expressed activator and repressor CfARFs and three CfARFs (CfARF3, 18, and 35) with gradually increased levels during leaf growth. Haplotype-resolved transcriptome analysis revealed that biallelic expression dominance is frequent among CfARFs and contributes to their gene expression patterns. In addition, co-expression network analysis identified the modules enriched with CfARFs. By establishing orthologous relationships among CfARFs, sorghum ARFs, and maize ARFs, we showed that CfARFs were mainly expanded by whole-genome duplications, and that the duplicated CfARFs might have been divergent due to differential expression and variations in domains and motifs. Our work provides a detailed catalog of CfARFs in lemongrass, representing a first step toward characterizing CfARF functions, and may be useful in molecular breeding to enhance lemongrass plant growth.

A report on identification of sequence polymorphism in barcode region of six commercially important Cymbopogon species.

CYMBOPOGON: is an important member of grass family Poaceae, cultivated for essential oils which have greater medicinal and industrial value. Taxonomic identification of Cymbopogon species is determined mainly by morphological markers, odour of essential oils and concentration of bioactive compounds present in the oil matrices which are highly influenced by environment. Authenticated molecular marker based taxonomical identification is also lacking in the genus; hence effort was made to evaluate potential DNA barcode loci in six commercially important Cymbopogon species for their individual discrimination and authentication at the species level. Four widely used DNA barcoding regions viz., ITS 1 & ITS 2 spacers, matK, psbA-trnH and rbcL were taken for the study. Gene sequences of the same or related genera of the concerned loci were mined from NCBI domain and primers were designed and validated for barcode loci amplification. Out of the four loci studied, sequences from matK and ITS spacer loci revealed 0.46% and 5.64% nucleotide sequence diversity, respectively whereas the other two loci i.e., psbA-trnH and rbcL showed 100% sequence homology. The newly developed primers can be used for barcode loci amplification in the genus Cymbopogon. The identified Single Nucleotide Polymorphisms from the studied sequences may be used as barcodes for the six Cymbopogon species. The information generated can also be utilized for barcode development of the genus by including more number of Cymbopgon species in future.

Autopolyploidy differentially influences body size in plants, but facilitates enhanced accumulation of secondary metabolites, causing increased cytosine methylation.

Whole genome duplication leads to autopolyploidy and brings about an increase in cell size, concentration of secondary metabolites and enhanced cytosine methylation. The increased cell size offers a positive advantage to polyploids for cell-surface-related activities, but there is a differential response to change in body size across species and taxonomic groups. Although polyploidy has been very extensively studied, having genetic, ecological and evolutionary implications, there is no report that underscores the significance of native secondary metabolites vis-à-vis body size with ploidy change. To address this problem we targeted unique diploid-autotetraploid paired sets of eight diverse clones of six species of Cymbopogon- a species complex of aromatic grasses that accumulate qualitatively different monoterpene essential oils (secondary metabolite) in their vegetative biomass. Based on the qualitative composition of essential oils and the plant body size relationship between the diploid versus autotetraploid paired sets, we show that polyploidy brings about enhanced accumulation of secondary metabolites in all cases, but exerts differential effects on body size in various species. It is observed that the accumulation of alcohol-type metabolites (e.g. geraniol) does not inhibit increase in body size with ploidy change from 2× to 4× (r = 0.854, P < 0.01), but aldehyde-type metabolites (e.g. citral) appear to drastically impede body development (r = -0.895). Such a differential response may be correlated to the metabolic steps involved in the synthesis of essential oil components. When changed to tetraploidy, the progenitor diploids requiring longer metabolic steps in production of their secondary metabolites are stressed, and those having shorter metabolite routes better utilize their resources for growth and vigour. In situ immunodetection of 5-methylcytosine sites reveals enhanced DNA methylation in autopolyploids. It is underpinned that the qualitative composition of secondary metabolites found in the vegetative biomass of the progenitor diploid has a decisive bearing on the body size of the derived autotetraploids and brings about an enhancement in genome-wide cytosine methylation.

Development and analysis of de novo transcriptome assemblies of multiple genotypes of Cymbopogon spp. reveal candidate genes involved in the biosynthesis of aromatic monoterpenes.

Despite the high economic value of the monoterpene-rich essential oils from different genotypes of Cymbopogon, the knowledge about the genes and metabolic route(s) involved in the biosynthesis of aromatic monoterpenes in this genus is limited. In the present study, a comprehensive transcriptome analysis of four genotypes of Cymbopogon, displaying diverse quantitative and qualitative profiles of volatile monoterpenes in their essential oils has been carried out. The comparative analysis of the deduced protein sequences corresponding to the transcriptomes of the four genotypes revealed 4609 genotype-specific orthogroups, which might contribute in defining genotype-specific phenotypes. The transcriptome data mining led to the identification of unigenes involved in the isoprenogenesis. The homology searches, combined with the phylogenetic and expression analyses provided information about candidate genes concerning the biosynthesis of monoterpene aldehyde, monoterpene alcohol, and monoterpene esters. In addition, the present study suggests a potential role of geranial reductase like enzyme in the biosynthesis of monoterpene aldehyde in Cymbopogon spp. The detailed analysis of the candidate pathway genes suggested that multiple enzymatic routes might be involved in the biosynthesis of aromatic monoterpenes in the genus Cymbopogon. The present study provides deeper insights into the biosynthesis of monoterpenes, which will be useful for the genetic improvement of these aromatic grasses.

Comparative transcriptional analysis of metabolic pathways and mechanisms regulating essential oil biosynthesis in four elite Cymbopogon spp.

Cymbopogon is an important aromatic and medicinal grass with several species of ethnopharmaceutical importance. The genus is extremely rich in secondary metabolites, monoterpenes like geraniol and citral being principal constituents, also used as biomarker for classification and identification of Cymbopogon chemotypes. In the light of this, present study involved RNA sequencing and comparison of expression profiles of four contrasting Cymbopogon species namely C. flexuosus var. Chirharit (citral rich and frost resistant), C. martinii var. PRC-1 (geraniol rich), C. pendulus var. Praman (the most stable and citral-rich genotype), and Jamrosa (a hybrid of C. nardus var. confertiflorus × C. jwarancusa (rich in geraniol and geranyl acetate). The transcriptome profiles revealed marked differences in gene expression patterns of 28 differentially expressed genes (DEGs) of terpenoid metabolic pathways between the four Cymbopogon sp. The major DEGs were Carotenoid Cleavage Dioxygenases (CCD), Aspartate aminotransferase (ASP amino), Mevalonate E-4 hydroxy, AKR, GGPS, FDPS, and AAT. In addition, few TFs related to different regulatory pathways were also identified. The gene expression profiles of DEGs were correlated to the EO yield and their monoterpene compositions. Overall, the PRC-1 (C. martinii) shows distinguished gene expression profiles from all other genotypes. Thus, the transcriptome sequence database expanded our understanding of terpenoid metabolism and its molecular regulation in Cymbopogon species. Additionally, this data also serves as an important source of knowledge for enhancing oil yield and quality in Cymbopogon and closely related taxa. KEY MESSAGE: Unfolding the new secretes surrounding EO biosynthesis and regulation in four contrasting Cymbopogon species.

Physical localization of 45S rDNA in Cymbopogon and the analysis of differential distribution of rDNA in homologous chromosomes of Cymbopogon winterianus.

Cymbopogon, commonly known as lemon grass, is one of the most important aromatic grasses having therapeutic and medicinal values. FISH signals on somatic chromosome spreads off Cymbopogon species indicated the localization of 45S rDNA on the terminal region of short arms of a chromosome pair. A considerable interspecific variation in the intensity of 45S rDNA hybridization signals was observed in the cultivars of Cymbopogon winterianus and Cymbopogon flexuosus. Furthermore, in all the varieties of C. winterianus namely Bio-13, Manjari and Medini, a differential distribution of 45S rDNA was observed in a heterologous pair of chromosomes 1. The development of C. winterianus var. Manjari through gamma radiation may be responsible for breakage of fragile rDNA site from one of the chromosomes of this heterologous chromosome pair. While, in other two varieties of C. winterianus (Bio-13 and Medini), this variability may be because of evolutionary speciation due to natural cross among two species of Cymbopogon which was fixed through clonal propagation. However, in both the situations these changes were fixed by vegetative method of propagation which is general mode of reproduction in the case of C. winterianus.

Ploidy-mediated reduced segregation facilitates fixation of heterozygosity in the aromatic grass, Cymbopogon martinii (Roxb.).

In most medicinal and aromatic plants, the vegetative tissue (e.g., roots, stems, leaves) is the source of the economic product. These plants are inherently heterozygous (natural allelic hybrids) and maintain their genetic makeup in nature by obligate vegetative propagation. Under seed cultivation, these plants incur population heterogeneity that reduces biomass and hampers product quality. Therefore, fixation of heterozygosity is vital for maintaining uniformity in quality of the economic product and quantity of biomass under seed cultivation. Although seed-grown clonal progenies identical to the mother plant can be obtained in certain plants that show an unusual breeding system called apomixis, such a breeding system is rare in medicinal and aromatic plants of economic value. Here we show an effective experimental strategy based on a polyploid model that facilitates fixation of heterozygosity in obligate asexual species owing to tetrasomic inheritance and low segregation in C(1) progenies from high-fertility C(0) autopolyploids. Using an obligate asexual species of aromatic grass-Cymbopogon martinii, we demonstrated that progenitor diploids with distal chiasma localization and low chiasmate association in meiosis, when changed into tetraploids, entail high gametic/seed fertility reflected in high bivalent pairing and balanced anaphase segregation. Their seed progenies evince crop homogeneity owing to reduced segregation, indicating fixation of heterozygosity present in the source diploids. Because C. martinii could be maintained through obligate vegetative propagation, here is a unique opportunity to utilize the polyploid advantage through C(1) seed progenies for commercial cultivation, as well as maintenance of original C(0) stock for raising seeds without losing polyploid heterosis normally threatened in subsequent segregating progenies on account of aneuploidy and gametic instability.

Comparative Analysis of In-Vitro Biological Activities of Methyl Eugenol Rich Cymbopogon khasianus Hack., Leaf Essential Oil with Pure Methyl Eugenol Compound.

BACKGROUND: The essential oil of methyl eugenol rich Cymbopogon khasianus Hack. was evaluated and its bioactivities were compared with pure methyl eugenol. So far, methyl eugenol rich essential oil of lemongrass was not studied for any biological activities; hence, the present study was conducted. OBJECTIVE: This study examined the chemical composition of essential oil of methyl eugenol rich Cymbopogon khasianus Hack., and evaluated its antioxidant, anti-inflammatory, antimicrobial, and herbicidal properties and genotoxicity, which were compared with pure compound, methyl eugenol. MATERIAL AND METHODS: Methyl eugenol rich variety of Cymbopogon khasianus Hack., with registration no. INGR18037 (c.v. Jor Lab L-9) was collected from experimental farm CSIR-NEIST, Jorhat, Assam (26.7378°N, 94.1570°E). The essential oil wasobtained by hydro-distillation using a Clevenger apparatus. The chemical composition of the essential oil was evaluated using GC/MS analysis and its antioxidant (DPPH assay, reducing power assay), anti-inflammatory (Egg albumin denaturation assay), and antimicrobial (Disc diffusion assay, MIC) properties, seed germination effect and genotoxicity (Allium cepa assay) were studied and compared with pure Methyl Eugenol compound (ME). RESULTS: Major components detected in the Essential Oil (EO) through Gas chromatography/mass spectroscopy analysis were methyl eugenol (73.17%) and ß-myrcene (8.58%). A total of 35components were detected with a total identified area percentage of 98.34%. DPPH assay revealed considerable antioxidant activity of methyl eugenol rich lemongrass essential oil (IC50= 2.263 µg/mL), which is lower than standard ascorbic acid (IC50 2.58 µg/mL), and higher than standard Methyl Eugenol (ME) (IC50 2.253 µg/mL). Methyl eugenol rich lemongrass EO showed IC50 38.00 µg/mL, ME 36.44 µg/mL, and sodium diclofenac 22.76 µg/mL, in in-vitro anti-inflammatory test. Moderate antimicrobial activity towards the 8 tested microbes was shown by methyl eugenol rich lemongrass essential oil whose effectiveness against the microbes was less as compared to pure ME standard. Seed germination assay further revealed the herbicidal properties of methyl eugenol rich essential oil. Moreover, Allium cepa assay revealed moderate genotoxicity of the essential oil. CONCLUSION: This paper compared the antioxidant, anti-inflammatory, antimicrobial, genotoxicity and herbicidal activities of methyl eugenol rich lemongrass with pure methyl eugenol. This methyl eugenol rich lemongrass variety can be used as an alternative of methyl eugenol pure compound. Hence, the essential oil of this variety has the potential of developing cost-effective, easily available antioxidative/ antimicrobial drugs but its use should be under the safety range of methyl eugenol and needs further clinical trials.

Geranyl acetate esterase controls and regulates the level of geraniol in lemongrass (Cymbopogon flexuosus Nees ex Steud.) mutant cv. GRL-1 leaves.

Essential oil isolated from lemongrass (Cymbopogon flexuosus) mutant cv. GRL-1 leaves is mainly composed of geraniol (G) and geranyl acetate (GA). The proportion of G and GA markedly fluctuates during leaf development. The proportions of GA and G in the essential oil recorded at day 10 after leaf emergence were approximately 59% and approximately 33% respectively. However, the level of GA went down from approximately 59 to approximately 3% whereas the level of G rose from approximately 33 to approximately 91% during the leaf growth period from day 10 to day 50. However, the decline in the level of GA was most pronounced in the early (day 10 to day 30) stage of leaf growth. The trend of changes in the proportion of GA and G has clearly indicated the role of an esterase that must be involved in the conversion of GA to G during leaf development. We isolated an esterase from leaves of different ages that converts GA into G and has been given the name geranyl acetate esterase (GAE). The GAE activity markedly varied during the leaf development cycle; it was closely correlated with the monoterpene (GA and G) composition throughout leaf development. GAE appeared as several isoenzymes but only three (GAE-I, GAE-II, and GAE-III) of them had significant GA cleaving activity. The GAE isoenzymes pattern was greatly influenced by the leaf developmental stages and so their GA cleaving activities. Like the GAE activity, GAE isoenzyme patterns were also found to be consistent with the monoterpene (GA and G) composition. GAE had an optimum pH at 8.5 and temperature at 30 degrees C. Besides GAE, a compound with phosphatase activity capable of hydrolyzing geranyl diphosphate (GPP) to produce geraniol has also been isolated.

Varietal Discrimination and Genetic Variability Analysis of Cymbopogon Using RAPD and ISSR Markers Analysis.

Cymbopogon is an important genus of family Poaceae, cultivated mainly for its essential oils which possess high medicinal and economical value. Several cultivars of Cymbopogon species are available for commercial cultivation in India and identification of these cultivars was conceded by means of morphological markers and essential oil constitution. Since these parameters are highly influenced by environmental factors, in most of the cases, it is difficult to identify Cymbopogon cultivars. In the present study, Random amplified polymorphic DNA (RAPD) and Inter-simple sequence repeat (ISSR) markers were employed to discriminate nine leading varieties of Cymbopogon since prior genomic information is lacking or very little in the genus. Ninety RAPD and 70 ISSR primers were used which generated 63 and 69 % polymorphic amplicons, respectively. Similarity in the pattern of UPGMA-derived dendrogram of RAPD and ISSR analysis revealed the reliability of the markers chosen for the study. Varietal/cultivar-specific markers generated from the study could be utilised for varietal/cultivar authentication, thus monitoring the quality of the essential oil production in Cymbopogon. These markers can also be utilised for the IPR protection of the cultivars. Moreover, the study provides molecular marker tool kit in both random and simple sequence repeats for diverse molecular research in the same or related genera.

Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus.

Advances in transcriptome sequencing provide fast, cost-effective and reliable approach to generate large expression datasets especially suitable for non-model species to identify putative genes, key pathway and regulatory mechanism. Citronella (Cymbopogon winterianus) is an aromatic medicinal grass used for anti-tumoral, antibacterial, anti-fungal, antiviral, detoxifying and natural insect repellent properties. Despite of having number of utilities, the genes involved in terpenes biosynthetic pathway is not yet clearly elucidated. The present study is a pioneering attempt to generate an exhaustive molecular information of secondary metabolite pathway and to increase genomic resources in Citronella. Using high-throughput RNA-Seq technology, root and leaf transcriptome was analysed at an unprecedented depth (11.7 Gb). Targeted searches identified majority of the genes associated with metabolic pathway and other natural product pathway viz. antibiotics synthesis along with many novel genes. Terpenoid biosynthesis genes comparative expression results were validated for 15 unigenes by RT-PCR and qRT-PCR. Thus the coverage of these transcriptome is comprehensive enough to discover all known genes of major metabolic pathways. This transcriptome dataset can serve as important public information for gene expression, genomics and function genomics studies in Citronella and shall act as a benchmark for future improvement of the crop.

El extracto acuoso de Cymbopogon citratus protege al ADN plasmídico del daño inducido por radiación UVC / Cymbopogon citratus aqueous extract protects plasmid DNA from UVC-induced damage

Objetivo: Evaluar el efecto protector del extracto acuoso de Cymbopogon citratus (DC) Stapf, ante el daño inducido por las radiaciones UVC. Material y Métodos: Para evaluar si el extracto acuoso de C. citratus era capaz de inducir roturas de cadenas en el ADN, moléculas de plásmido pBluescript SK II fueron tratadas con diferentes concentraciones del extracto (0,01 - 4,0 mg/mL), en los tiempos de exposición: 30, 60 y 90 min. El efecto fotoprotector fue evaluado aplicando el extracto vegetal antes, durante, y después de la irradiación del ADN plasmídico con 200 J/m2 de UVC. La actividad enzimática de T4 endonucleasa V fue empleada para detectar formación de CPDs. Las formas superenrollada y relajada de las moléculas de plásmido fueron separadas electroforéticamente en gel de agarosa. Adicionalmente, se midió la transmitancia del extracto acuoso a la DO de 254 nm. Resultados: Ninguna de las concentraciones evaluadas resultó genotóxica con 30 min de tratamiento. Las concentraciones ≥ 2 mg/mL indujeron roturas de cadenas a los 90 min de incubación. El extracto de C. citratus a concentraciones ≥ 0,5 mg/mL protegió al ADN frente a las radiaciones UVC. Conclusiones: En nuestras condiciones experimentales, el extracto acuoso de C. citratus protege al ADN frente a la genotoxicidad inducida por la luz UVC, previniendo la generación de CPDs, pero no es capaz de eliminarlas una vez formadas

Aim: to evaluate the photoprotective effect of aqueous extract of Cymbopogon citratus (DC) Stapf against UVC-induced damage to ADN. Material and methods: In the experimental procedure, samples of plasmid pBluescript SK II solutions were exposed to C. citratus aqueous extract in 0.01-4.0 mg/mL concentrations during 30, 60 and 90 min. In order to evaluate the photoprotective effect, the vegetal extract was applied before, during and after UVC radiation at 200 J/m2 doses. DNA repair enzymes T4 endonuclease V was employed in order to discriminate CPDs damage. Then, supercoiled and relaxed forms of DNA were separated after electrophoretic migration in agarose gels. Also aqueous extract transmittance was measure at 254 nm OD. Results: None of the concentrations tested were genotoxic in 30 min of exposition. Concentrations ≥ 2 mg/mL induced strand breaks at 90 min of incubation. The C. citratus extract at concentrations ≥ 0.5 mg/ mL protect DNA in front of UVC radiation. Conclusions: In our experimental conditions, C. citratus extract protects DNA from the genotoxicity induced by light UVC, preventing the CPDs generation, but is not able to eliminate DNA damage once formed

Development of simple sequence repeat markers in cymbopogon species.

The genus Cymbopogon comprises about 140 species, which produce characteristic aromatic essential oils. However, the phenotypic identification of species of Cymbopogon has been difficult as a result of widespread occurrence of natural variants, which differ in ploidy levels and chemotaxonomic complexities. Therefore, we have developed a set of simple sequence repeat markers from a genomic library of Cymbopogon jwarancusa to help in the precise identification of the species (including accessions) of Cymbopogon. For this purpose, we isolated 16 simple sequence repeat containing genomic deoxyribonucleic acid clones of C. jwarancusa, which contained a total of 32 simple sequence repeats with a range of 1 to 3 simple sequence repeats per clone. The majority (68.8%) of the 32 simple sequence repeats comprised dinucleotide repeat motifs followed by simple sequence repeats with trinucleotide (21.8%) and other higher order repeat motifs. Eighteen (81.8%) of the 22 designed primers for the above simple sequence repeats amplified products of expected sizes, when tried with genomic DNA of C. jwarancusa, the source species. Thirteen (72.2%) of the 18 functional primers detected polymorphism among the three species of Cymbopogon (C. flexuosus, C. pendulus and C. jwarancusa) and amplified a total of 95 alleles (range 1-18 alleles) with a PIC value of 0.44 to 0.96 per simple sequence repeat. Thus, the higher allelic range and high level of polymorphism demonstrated by the newly developed simple sequence repeat markers are likely to have many applications such as in improvement of essential oil quality by authentication of Cymbopogon species and varieties and mapping or tagging the genes controlling agronomically important traits of essential oils, which can further be utilized in marker assisted breeding.