A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal.

Natural spices play an essential role in human nutrition and well-being. However, their processing on different scales can expose them to potential sources of contamination. This study aimed to describe the bacterial community genomic footprint in spices sold in Senegal. Spice samples were collected in August 2022 in Saint-Louis, Senegal. The genomic region coding bacterial 16S rRNA was then amplified and sequenced using Oxford Nanopore Technology (ONT). Sequencing was carried out on two batches of samples, one containing part of the "Local Spices or Herbs" (n = 10), and the other, a mixture of 7 spices, Curcuma, Thyme and the other part of the "Local Spices or Herbs" (n = 39). Results showed high bacterial diversity and the predominance of Escherichia coli and Salmonella enterica in samples, with total reads of 65,744 and 165,325 for the two batches, respectively. The sample category "Homemade mixture of food condiments ", which includes all "Local Spices or Herbs" samples, showed remarkable bacterial diversity. These were followed by Curcuma, a blend of 7 spices and thyme. Also, the different categories of spices studied show similarities in their bacterial composition. These results highlight the microbial community's highly diverse genomic profile, including pathogenic bacteria, in spice samples.

Identification and functional analysis of floral terpene synthase genes in Curcuma alismatifolia.

MAIN CONCLUSION: CaTPS2 and CaTPS3 were significantly expressed in flowers of Curcuma alismatifolia 'Shadow' and demonstrated bifunctional enzyme activity, CaTPS2 generated linalool and nerolidol as products, and CaTPS3 catalyzed ß-myrcene and ß-farnesene formation. This study presents the discovery and functional characterization of floral terpene synthase (TPS) genes in Curcuma alismatifolia 'Shadow', a cultivar renowned for its unique fragrance. Addressing the gap in understanding the genetic basis of floral scent in this species, we identified eight TPS genes through comprehensive transcriptome sequencing. Among these, CaTPS2 and CaTPS3 were significantly expressed in floral tissues and demonstrated bifunctional enzyme activity corresponding to the major volatile compounds detected in 'Shadow'. Functional analyses, including in vitro assays complemented with rigorous controls and alternative identification methods, elucidated the roles of these TPS genes in terpenoid biosynthesis. In vitro studies were conducted via heterologous expression in E. coli, followed by purification of the recombinant protein using affinity chromatography, enzyme assays were performed with GPP/FPP as the substrate, and volatile products were inserted into the GC-MS for analysis. Partially purified recombinant protein of CaTPS2 catalyzed GPP and FPP to produce linalool and nerolidol, respectively, while partially purified recombinant protein of CaTPS3 generated ß-myrcene and ß-farnesene with GPP and FPP as substrates, respectively. Real-time quantitative PCR further validated the expression patterns of these genes, correlating with terpenoid accumulation in different plant tissues. Our findings illuminate the molecular mechanisms underpinning floral fragrance in C. alismatifolia and provide a foundation for future genetic enhancements of floral scent in ornamental plants. This study, therefore, contributes to the broader understanding of terpenoid biosynthesis in plant fragrances, paving the way for biotechnological applications in horticulture plant breeding.

Study on the genetic variability and adaptability of turmeric (Curcuma longa L.) genotypes for development of desirable cultivars.

Turmeric, a globally cultivated spice, holds significance in medicine, and cosmetics, and is also a very popular ingredient in South Asian cuisine. A study involving 53 turmeric genotypes evaluated for rhizome yield and related traits at Spices Research Center, Bogura, Bangladesh over three years (2019-22). A randomized complete block design was followed with two replications. ANOVA revealed significant trait variations among genotypes. Genotype T0015 emerged as the highest yielder at 28.04 t/ha. High heritability (0.58-0.99) and genetic advance characterized plant height (PH), mother rhizome weight (WMR), primary and secondary finger weights (WPF and WSF), and yield per plant (YPP) across seasons. Genetic gain (GG) was prominent in these traits. Genotypic and phenotypic coefficient variations (GCV and PCV) (6.24-89.46 and 8.18-90.88, respectively) across three years highlighted mother rhizome weight's importance followed by numbers of primary finger (NPF), and WPF. Positive and significant correlations, especially with PH, WMR, WPF, and YPP, emphasized their relevance to fresh yield (FY). Multiple linear regression identified PH, number of mother rhizome (NMR) and WMR as key contributors, explaining 37-79% of FY variability. Cluster analysis grouped genotypes into five clusters with maximum distance observed between clusters II and III. The geometric adaptability index (GAI) assessed adaptability and superiority, revealing nine genotypes outperforming the best existing cultivar. Genotype T0117 as the top performer based on GAI, followed by T0103 and T0094. Mean rank analysis favoured T0121 as the best performer, succeeded by T0117, T0082 and T0106. The top ten genotypes (T0015, T0061, T0082, T0085, T0094, T0103, T0106, T0117, T0121 and T0129) were identified as superior based on yield and overall ranking, warranting further evaluation. These findings may induce a window for improving turmeric research and ultimately play a role in enhancing its cultivation and productivity.

Molecular genetic divergence analysis amongst high curcumin lines of Golden Crop (Curcuma longa L.) using SSR marker and use in trait-specific breeding.

Curcuma longa L., is recognized worldwide as a medicinally and economically important plant species due to its curcumin content which is an industrially important compound. In this study, a total of 329 accessions were collected from four states of India and planted in the experimental farm of CSIR-NEIST, Jorhat, India, in augmented design. Among these, 152 high curcumin (> 1.50%) accessions were screened for molecular divergence study using 39 SSR primers. The primers showed the most efficient outcome with 2-8 allele/ loci and a total 163 number of alleles with 100% polymorphism. Cluster analysis revealed the construction of three clusters, out of which one cluster was geographically dependent, and germplasm was particularly from Assam state. Jaccard's pairwise coefficient showed maximum genetic dissimilarity of (0.75) between accession RRLJCL 3 and RRLJCL 126, indicating high variation as it was from two different states viz Arunachal Pradesh and Nagaland respectively and minimum genetic dissimilarity of (0.09) between RRLJCL 58 and RRLJCL 59 indicating significantly less variation as the two accessions were from same state, i.e., Arunachal Pradesh. Analysis of Molecular Variance (AMOVA) revealed high molecular variation within the population (87%) and significantly less variation among the population (13%). Additionally, Neighbour Joining dendrogram, Principal Component Analysis (PCA), and bar plot structure revealed similar clustering of germplasm. This diversity assessment will help in selecting the trait-specific genotypes, crop improvement program, conservation of gene pool, marker-assisted breeding, and quantitative trait loci identification. Moreover, to the best of our knowledge, it is the first molecular diversity report among 152 high curcumin lines of C. longa from North East India using 39 SSR primers.

Differential gene expression analysis under salinity stress in the selected turmeric (Curcuma longa L.) cultivars for curcuminoid biosynthesis.

BACKGROUND: Curcuminoids are the phenolic compounds found exclusively in turmeric. Their presence is known to increase immunity and resistance against certain cancers and neurological disorders in humans also, protecting the plant itself against salinity stress. METHODS: In this experiment, we studied the expression levels of MAPK1 and DCS genes, their curcuminoid biosynthesis under salinity stress conditions so that the impact of individual genes can be understood using semi- quantitative PCR. RESULTS: The expressions of the genes with respect to curcuminoid biosynthesis showed fluctuations in their band intensity values due to the production of curcuminoids, which is initiated first in the leaves followed by the rhizomes. Not all the genes responsible for the curcuminoid biosynthesis show positive regulation under salt stress conditions which is observed in response to the severity of the stress imposed on the cultivars. CONCLUSIONS: In our findings, both the genes MAPK1 and DCS were down-regulated for curcuminoid biosynthesis compared to their controls in both the cultivars Vallabh Sharad and Selection 1.

Comparative Plastomes of Curcuma alismatifolia (Zingiberaceae) Reveal Diversified Patterns among 56 Different Cut-Flower Cultivars.

Curcuma alismatifolia (Zingiberaceae) is an ornamental species with high economic value due to its recent rise in popularity among floriculturists. Cultivars within this species have mixed genetic backgrounds from multiple hybridization events and can be difficult to distinguish via morphological and histological methods alone. Given the need to improve identification resources, we carried out the first systematic study using plastomic data wherein genomic evolution and phylogenetic relationships from 56 accessions of C. alismatifolia were analyzed. The newly assembled plastomes were highly conserved and ranged from 162,139 bp to 164,111 bp, including 79 genes that code for proteins, 30 tRNA genes, and 4 rRNA genes. The A/T motif was the most common of SSRs in the assembled genomes. The Ka/Ks values of most genes were less than 1, and only two genes had Ka/Ks values above 1, which were rps15 (1.15), and ndhl (1.13) with petA equal to 1. The sequence divergence between different varieties of C. alismatifolia was large, and the percentage of variation in coding regions was lower than that in the non-coding regions. Such data will improve cultivar identification, marker assisted breeding, and preservation of germplasm resources.

Ancient hybridization in Curcuma (Zingiberaceae)-Accelerator or brake in lineage diversifications?

Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored. Here, we present an account of several events of ancient hybridization in turmeric, the economically important plant genus Curcuma (Zingiberaceae), which harbors about 130 known species. We analyzed 1094 targeted low-copy genes and plastomes obtained by next-generation sequencing of 37 species of Curcuma, representing the known genetic diversity and spanning the geographical distribution of the genus. Using phylogenetic network analysis, we show that the entire genus Curcuma as well as its most speciose lineage arose via introgression from the genus Pyrgophyllum and one of the extinct lineages, respectively. We also document a single event of ancient hybridization, with C. vamana as a product, that represents an evolutionary dead end. We further discuss distinct circumstances of those hybridization events that deal mainly with (in)congruence in chromosome counts of the parental lineages.

Identification and Registration for High-Yielding Strain through ST and MLT of Curcuma caesia Roxb. (Jor Lab KH-2): A High-Value Medicinal Plant.

(1) Background: Curcuma caesia Roxb. is a high valued crop which is extensively used in pharmaceuticals, flavour and fragrances. C. caesia is recognised as an endangered species due to its extensive collection from the wild through human intervention. Therefore, to prevent the species from extinction, it is very necessary to conserve and cultivate this plant species for the sustainable availability of the raw material. (2) Methods: In the present plant breeding programme, a multi-year study was performed for the identification of superior genotypes which will help in conservation. To fulfil this objective, a total of 135 accessions of C. caesia were collected from different regions of India and were set up for experimental selection trial for three years (2016-2018). After proper evaluation of the genotypes based on six agronomical traits, five high-yielding genotypes were identified which underwent multilocation trial for two years (2019 and 2020). The stability analysis using the Eberhart-Russell method, AMMI and GGE biplot were used to study the consistency of the genotypes in varied environments compared with the check variety. (3) Results: Analysis of variance indicated significant genotype and environment interaction for the yield traits, i.e., dry rhizome recovery, rhizome yield and essential oil yield. The coefficient of variation (CV) was highest for tillers per plant (21.76) and lowest for the plant height (4.93). All the results clearly demonstrated Jor Lab KH-2 as the highest yielding and stable genotype in varied environments compared with the check variety and other selected genotypes. (4) Conclusions: This genotype was then submitted to ICAR-NBPGR, New Delhi, for germplasm registration and received its confirmation vide registration number INGR 21159. This genotype will greatly benefit the breeders and will also help in the conservation of this endangered species. This is the first report on the identification and registration of a high-yielding variety of C. caesia.

Comparative transcriptome analysis on drought stress-induced floral formation of Curcuma kwangsiensis.

The rhizomes and tubers of Curcuma kwangsiensis have extensive medicinal value in China. However, the inflorescences of C. kwangsiensis are rarely known in horticulture, because of its low field flowering rate. In order to improve the flowering rate of C. kwangsiensis, we conducted drought stress treatment on the rhizome of C. kwangsiensis. The flowering rate of rhizome was the highest after 4d of drought stress treatment, and the buds on the rhizome could be obviously swell on the 4th day of rehydration culture. In order to identify the genes regulating the flowering time of Curcuma kwangsiensis, comparative transcriptome analysis was performed on the buds on rhizomes before drought stress treatment, 4 d after drought stress treatment and 4 d after rehydration culture. During this process, a total of 20 DEGs controlling flowering time and 23 DEGs involved in ABA synthesis and signal transduction were identified, which might regulate the flowering of C. kwangsiensis under drought stress. Some floral integration factors, such as SOC1 and FTIP, were up-regulated under drought stress for 4 d, indicating that C. kwangsiensis had flowering trend under drought stress. The results of the present study will provide theoretical support for the application of Curcuma kwangsiensis in gardening.

Transcriptome analysis reveals regulation mechanism of methyl jasmonate-induced terpenes biosynthesis in Curcuma wenyujin.

Curcuma wenyujin is the source plant of three traditional Chinese medicines, which have been widely used in clinical treatment over 1000 years. The content of terpenes, the major medicinal active ingredients, is relatively low in this plant. Studies have shown that MeJA can promote terpenes biosynthesis in plants. However, the mechanism underlying the effect of MeJA in C. wenyujin remains unclear. In this work, the transcriptome of C. wenyujin leaves with MeJA treatment was analyzed to elucidate the regulation mechanism of MeJA-mediated terpene biosynthesis. Based on the RNA-seq data, 7,246 unigenes were differentially expressed with MeJA treatment. Expression pattern clustering of DEGs revealed that unigenes, related to JA biosynthesis and signal transduction, responded to exogenous MeJA stimulation on the early stage and maintained throughout the process. Subsequently, unigenes related to terpene biosynthesis pathway showed a significant up-regulation with 6 h treatment. The analysis results suggested that MeJA induced the expression of JA biosynthesis genes (such as LOXs, AOSs, AOCs, OPRs, and MFPs) and JA signal transduction core genes (JAZs and MYCs) to activate JA signaling pathway. Meanwhile, downstream JA-responsive genes presented up-regulated expression levels such as AACT, HMGSs, HMGRs, DXSs, DXRs, MCTs, HDSs, and HDRs, thus promoting terpenes biosynthesis. The transcriptional expressions of these genes were validated by qRT-PCR. In addition, six CwTPS genes in response to MeJA were identified. With MeJA treatment, the expression levels of CwTPSs were increased as well as those of the transcription factors MYB, NAC, bZIP, WRKY, AP2/ERF, and HLH. These TFs might potentially regulate terpenes biosynthesis. These results provide insights for regulation mechanism of terpenes biosynthesis.

Discrimination of Curcuma species from Asia using intron length polymorphism markers in genes encoding diketide-CoA synthase and curcumin synthase.

Recently, Curcuma rhizome-related foods with claimed health benefits have been used worldwide; however, correct identification and quality assessment have not been conducted. Due to the wide distribution and morphological similarities of Curcuma species, the classification of some species is debated and nomenclature is inconsistent among countries. In this study, to elucidate specific molecular markers of medicinally used Curcuma species in Asia, and to solve the confusion on the reported botanical origin of crude drugs, molecular analysis based on the intron length polymorphism (ILP) in genes encoding diketide-CoA synthase and curcumin synthase and the trnK intron sequences was performed using 59 plant specimens and 42 crude drug samples from 13 Curcuma species, obtained from Asian countries. The ILP patterns of the respective species from both plant specimens and crude drug samples revealed high consistency in C. aromatica, C. zedoaria, C. phaeocaulis, C. aeruginosa, C. wenyujin, and C. zanthorrhiza, but showed intraspecies polymorphism in C. longa, C. kwangsiensis, C. amada, C. mangga and C. comosa. The C. longa specimens and samples were separated into three subgroups which were highly consistent with their geographical origins. Based on the ILP markers and the trnK intron sequences, the botanical origins of "Khamin oi" from Thailand were correctly determined to be C. longa or a hybrid between C. longa and other species, and "Wan narn kum" from Thailand and "Kasturi manjal" from India were correctly determined to be C. zanthorrhiza.

Genetic analysis of Curcuma species from Asia based on intron regions of genes encoding diketide-CoA synthase and curcumin synthase.

Intron length polymorphism (ILP) markers in genes encoding diketide-CoA synthase (DCS) and curcumin synthase (CURS) showed high identification rates in 13 Curcuma species from Asia. However, the sequences of the intron regions have not yet been analyzed. To elucidate the sequence differences in intron regions of the DCS and CURS genes and to search for specific sequences suitable for the identification of Curcuma species, a large number of sequences were determined through subcloning coupled with sequencing analysis of six Curcuma plant specimens belonging to five species that showed distinct ILP patterns. More than 30 sequences of each region from each specimen were grouped into genes DCS1, DCS2, or CURS1-3 and subsequently the sequences of the same genes were compared. Sequences belonging to the same gene showed inter-species similarity, and thus, these intron sequences were less informative within each single-gene region. The determined sequences from each specimen showed 3-5 kinds of sequence lengths in DCS intron I region, and 5-7 kinds of sequence lengths in CURS intron region. The length of determined sequences and the fragment number in each intron region were different among species, or specimens in C. longa, which were in accordance with the fragment lengths and numbers in their corresponding ILP patterns.

Genome sequencing of turmeric provides evolutionary insights into its medicinal properties.

Curcuma longa, or turmeric, is traditionally known for its immense medicinal properties and has diverse therapeutic applications. However, the absence of a reference genome sequence is a limiting factor in understanding the genomic basis of the origin of its medicinal properties. In this study, we present the draft genome sequence of C. longa, belonging to Zingiberaceae plant family, constructed using 10x Genomics linked reads and Oxford Nanopore long reads. For comprehensive gene set prediction and for insights into its gene expression, transcriptome sequencing of leaf tissue was also performed. The draft genome assembly had a size of 1.02 Gbp with ~70% repetitive sequences, and contained 50,401 coding gene sequences. The phylogenetic position of C. longa was resolved through a comprehensive genome-wide analysis including 16 other plant species. Using 5,388 orthogroups, the comparative evolutionary analysis performed across 17 species including C. longa revealed evolution in genes associated with secondary metabolism, plant phytohormones signaling, and various biotic and abiotic stress tolerance responses. These mechanisms are crucial for perennial and rhizomatous plants such as C. longa for defense and environmental stress tolerance via production of secondary metabolites, which are associated with the wide range of medicinal properties in C. longa.

Transcriptome sequencing and functional characterization of new sesquiterpene synthases from Curcuma wenyujin.

Tubers of Curcuma wenyujin are rich in essential oils, mainly various sesquiterpenes, showing antibacterial, anti-viral and anti-tumor effects. However, the molecular mechanism of C. wenyujin is deficient and related sesquiterpene synthases are still unclear. In this study, the transcriptome data of tubers and leaves from C. wenyujin were obtained and assembled into 78 092 unigenes. Of them, 244 unigenes were predicted to be involved in terpenoid biosynthesis while 131 unigenes were categorized as the "Terpenoid backbone biosynthesis" (TBB) term. Twenty-two unigenes possessed terpene synthase domain; five were predicted to be sesquiterpene synthases. Of the 208 unigenes annotated as cytochromes P450, 8 unigenes with full-length coding sequences were part of the CYP71 clade that primarily may perform hydroxylations of specialized metabolites. Furthermore, Ten DEGs related to the C5 precursor supply and sesquiterpene synthesis were validated by Real-time PCR; that showed a close correspondence with transcriptome sequence. A novel germacrene B synthase (CwGBS) and α-santalene synthase (CwSS) were identified in metabolically engineering E. coli. This study provided the first de novo transcriptome comparative analysis of leaf and tuber tissues from C. wenyujin, aiming to understand genetic mechanisms. Key genes involved in the biosynthesis of sesquiterpene will help for revealing the underlying mechanisms of C. wenyujin.

Transcriptomic analysis to reveal the differentially expressed miRNA targets and their miRNAs in response to Ralstonia solanacearum in ginger species.

BACKGROUND: Bacterial wilt is the most devastating disease in ginger caused by Ralstonia solanacearum. Even though ginger (Zingiber officinale) and mango ginger (Curcuma amada) are from the same family Zingiberaceae, the latter is resistant to R. solanacearum infection. MicroRNAs have been identified in many crops which regulates plant-pathogen interaction, either through silencing genes or by blocking mRNA translation. However, miRNA's vital role and its targets in mango ginger in protecting bacterial wilt is not yet studied extensively. In the present study, using the "psRNATarget" server, we analyzed available ginger (susceptible) and mango ginger (resistant) transcriptome to delineate and compare the microRNAs (miRNA) and their target genes (miRTGs). RESULTS: A total of 4736 and 4485 differential expressed miRTGs (DEmiRTGs) were identified in ginger and mango ginger, respectively, in response to R. solanacearum. Functional annotation results showed that mango ginger had higher enrichment than ginger in top enriched GO terms. Among the DEmiRTGs, 2105 were common in ginger and mango ginger. However, 2337 miRTGs were expressed only in mango ginger which includes 62 defence related and upregulated miRTGs. We also identified 213 miRTGs upregulated in mango ginger but downregulated in ginger, out of which 23 DEmiRTGS were defence response related. We selected nine miRNA/miRTGs pairs from the data set of common miRTGs of ginger and mango ginger and validated using qPCR. CONCLUSIONS: Our data covered the expression information of 9221 miRTGs. We identified nine miRNA/miRTGs key candidate pairs in response to R. solanacearum infection in ginger. This is the first report of the integrated analysis of miRTGs and miRNAs in response to R. solanacearum infection among ginger species. This study is expected to deliver several insights in understanding the miRNA regulatory network in ginger and mango ginger response to bacterial wilt.

Transcriptome analysis of Curcuma wenyujin from Haikou and Wenzhou, and a comparison of the main constituents and related genes of Rhizoma Curcumae.

For more than a thousand years, Rhizoma Curcumae (known as E zhu), a Chinese herbal medicine, has been used to eradicate blood stasis and relieve aches. The plant Curcuma wenyujin, which is grown primarily in Wenzhou, China, is considered the best source of Rhizoma Curcumae. In this study, we sought to ascertain differences in transcript profiles of C. wenyujin grown in traditional (Wenzhou) and recently established (Haikou) production areas based on Illumina and RNA (RNA-seq) sequencing. We also examined differences in the main components of the volatile oil terpene; curcumin, polysaccharide, and starch constituents and related genes in the corresponding pathways, in C. wenyujin cultivated in the two production areas. We accordingly found that the essential oil (2.05%), curcumin (1.46%), and polysaccharide (8.90%) content in Wenzhou rhizomes was higher than that in the rhizomes of plants from Haikou (1.60%, 0.91%, and 6.15%, respectively). In contrast, the starch content of Wenzhou rhizomes (17.0%) was lower than that of Haikou rhizomes (23.8%). Furthermore, we detected significant differences in the oil components of Haikou and Wenzhou rhizomes, with curzerene (32.34%), curdione (21.35%), and germacrene B (9.39%) being the primary components of the essential oil derived from Wenzhou rhizomes, and curzerene (20.13%), curdione (14.73%), and cineole (9.76%) being the main constituents in Haikou rhizomes. Transcriptome and qPCR analyses revealed considerable differences in gene expression between Wenzhou and Haikou rhizomes. The expression of terpene, curcumin, and polysaccharide pathway-related genes in Wenzhou rhizomes was significantly up-regulated, whereas the expression of starch-associated genes was significantly down-regulated, compared with those in Haikou rhizomes. Difference in the content of terpene, curcumin, polysaccharides, and starch in rhizomes from the two production areas could be explained in terms of differences in expression of the related genes.

Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution.

Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.

An integrated strategy to identify genes responsible for sesquiterpene biosynthesis in turmeric.

KEY MESSAGE: Metabolic module, gene expression pattern and PLS modeling were integrated to precisely identify the terpene synthase responsible for sesquiterpene formation. Functional characterization confirmed the feasibility and sensitivity of this strategy. Plant secondary metabolite biosynthetic pathway elucidation is crucial for the production of these compounds with metabolic engineering. In this study, an integrated strategy was employed to predict the gene function of sesquiterpene synthase (STS) genes using turmeric as a model. Parallel analysis of gene expression patterns and metabolite modules narrowed the candidates into an STS group in which the STSs showed a similar expression pattern. The projections to latent structures by means of partial least squares model was further employed to establish a clear relationship between the candidate STS genes and metabolites and to predict three STSs (ClTPS16, ClTPS15 and ClTPS14) involved in the biosynthesis of several sesquiterpene skeletons. Functional characterization revealed that zingiberene and ß-sesquiphellandrene were the major products of ClTPS16, and ß-eudesmol was produced by ClTPS15, both of which indicated the accuracy of the prediction. Functional characterization of a control STS, ClTPS1, produced a small amount of ß-sesquiphellandrene, as predicted, which confirmed the sensitivity of metabolite module analysis. This integrated strategy provides a methodology for gene function predictions, which represents a substantial improvement in the elucidation of biosynthetic pathways in nonmodel plants.

De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.

Introducing curcumin biosynthesis in Arabidopsis enhances lignocellulosic biomass processing.

Lignin is the main cause of lignocellulosic biomass recalcitrance to industrial enzymatic hydrolysis. By partially replacing the traditional lignin monomers by alternative ones, lignin extractability can be enhanced. To design a lignin that is easier to degrade under alkaline conditions, curcumin (diferuloylmethane) was produced in the model plant Arabidopsis thaliana via simultaneous expression of the turmeric (Curcuma longa) genes DIKETIDE-CoA SYNTHASE (DCS) and CURCUMIN SYNTHASE 2 (CURS2). The transgenic plants produced a plethora of curcumin- and phenylpentanoid-derived compounds with no negative impact on growth. Catalytic hydrogenolysis gave evidence that both curcumin and phenylpentanoids were incorporated into the lignifying cell wall, thereby significantly increasing saccharification efficiency after alkaline pretreatment of the transgenic lines by 14-24% as compared with the wild type. These results demonstrate that non-native monomers can be synthesized and incorporated into the lignin polymer in plants to enhance their biomass processing efficiency.