Identification and functional characterization of three new terpene synthase genes involved in chemical defense and abiotic stresses in Santalum album

Identification of 3-hydroxy-3-methylglutaryl monoacyl-coenzyme A reductase (HMGR) associated with the synthesis of terpenoids in Santalum album L

Santalum album is an economically important plant in the craft, spices and medicine industries. The main chemical constituents found in sandalwood essential oils are sesquiterpenes. 3-Hydroxy-3-methylglutaryl monoacyl-coenzyme A reductase (HMGR) is one of the rate-limiting enzymes required for the synthesis of sandal sesquiterpenes, but there are no studies on the HMGR gene in S. album. In this study, the full-length ORFs of the upper rate-limiting enzyme genes SaHMGR1 and SaHMGR2, which lie upstream of the MVA metabolic pathway of sandal sesquiterpenes, were cloned for the first time. Bioinformatics and phylogenetic analyses were conducted. The results showed that SaHMGR1 and SaHMGR2 had typical domains of HMGR class I enzymes in the HMGR superfamily, including four catalytic sites, six NADPH-binding sites, five substrate binding regions, four inhibitor binding sites, and several dimer interface regions. A phylogenetic analysis showed that SaHMGR1 and SaHMGR2 were highly conserved relative to corresponding genes in other plants. An analysis of subcellular localization showed that these SaHMGR genes were located in the endoplasmic reticulum. SaHMGR1 and SaHMGR2 were detected by real-time PCR in roots, sapwood, heartwood, young leaves, mature leaves and twigs. Highest expression was in roots. SaHMGR1 expression was higher in mature leaves than in heartwood while SaHMGR2 expression was lower in mature leaves than in heartwood. Expression in Escherichia coli strain DH5α with plasmid pET-32a (+) was also used to verify the functionality of both HMGR proteins, which catalyzed the formation of MVA from HMG-CoA. In E. coli, the enzymatic activity of SaHMGR1 was higher than that of SaHMGR2. These findings provide a basis for further studies on the function of SaHMGR genes and the regulation of sesquiterpene biosynthesis in S. album.

Functional characterization of a novel terpene synthase GaTPS1 involved in (E)-α-bergamotene biosynthesis in Gossypium arboreum

Terpenoids in plants are mainly synthesized by terpene synthases (TPSs), which play an important role in plant-environment interactions. Gossypium arboreum is one of the important cotton cultivars with excellent pest resistance, however, the biosynthesis of most terpenoids in this plant remains unknown. In this study, we performed a comparative transcriptome analysis of leaves from intact and Helicoverpa armigera-infested cotton plants. The results showed that the H. armigera infestation mainly induced the JA signaling pathway, ten TPS genes were differentially expressed in G. arboreum leaves. Among them, a novel terpene synthase, GaTPS1, was heterologously expressed and functionally characterized in vitro. The enzymatic reaction indicated that recombinant GaTPS1 was primarily responsible for the production of (E)-α-bergamotene. Moreover, molecular docking and site-directed mutagenesis analysis demonstrated that two amino acid residues, A412L and Y535F, distinctly influenced the catalytic activities and product specificity of GaTPS1. The mutants GaTPS1-A412L and GaTPS1-Y535F resulted in a decrease in the proportion of products (E)-α-bergamotene and D-limonene, while an increase in the proportion of products (E)-β-farnesene, α-pinene and β-myrcene. Our findings provide valuable insights into understanding the molecular basis of terpenoid diversity in G. arboreum, with potential applications in plant metabolism regulation and the improvement of resistant cotton cultivars.

Chromosome-scale genome assembly of Docynia delavayi provides new insights into the α-farnesene biosynthesis

Docynia delavayi is an economically significant fruit species with a high market potential due to the special aroma of its fruit. Here, a 653.34 Mb high-quality genome of D. delavayi was first reported, of which 93.8 % of the sequences (612.98 Mb) could be anchored to 17 chromosomes, containing 48,325 protein-coding genes. Ks analysis proved that two whole genome duplication (WGD) events occurred in D. delavayi, resulting in the expansion of genes associated with terpene biosynthesis, which promoted its fruit-specific aroma production. Combined multi-omics analysis, α-farnesene was detected as the most abundant aroma substance emitted by D. delavayi fruit during storage, meanwhile one α-farnesene synthase gene (AFS) and 15 transcription factors (TFs) were identified as the candidate genes potentially involved in α-farnesene biosynthesis. Further studies for the regulation network of α-farnesene biosynthesis revealed that DdebHLH, DdeERF1 and DdeMYB could activate the transcription of DdeAFS. To our knowledge, it is the first report that MYB TF plays a regulatory role in α-farnesene biosynthesis, which will greatly facilitate future breeding programs for D. delavayi.

Identification of Transcription Factors of Santalene Synthase Gene Promoters and SaSSY Cis-Elements through Yeast One-Hybrid Screening in Santalum album L

The main components of sandalwood heartwood essential oil are terpenoids, approximately 80% of which are α-santalol and β-santalol. In the synthesis of the main secondary metabolites of sandalwood heartwood, the key gene, santalene synthase (SaSSY), can produce α-santalene and β-santalene by catalyzed (E, E)-FPP. Furthermore, santalene is catalyzed by the cytochrome monooxygenase SaCYP736A167 to form sandalwood essential oil, which then produces a fragrance. However, the upstream regulatory mechanism of the key gene santalene synthase remains unclear. In this study, SaSSY (Sal3G10690) promoter transcription factors and SaSSY cis-elements were screened. The results showed that the titer of the sandalwood cDNA library was 1.75 × 107 CFU/mL, 80% of the inserted fragments identified by PCR were over 750 bp in length, and the positivity rate of the library was greater than 90%. The promoter region of the SaSSY gene was shown to have the structural basis for potential regulatory factor binding. After sequencing and bioinformatics analysis, we successfully obtained 51 positive clones and identified four potential SaSSY transcriptional regulators. Sal6G03620 was annotated as the transcription factor MYB36-like, and Sal8G07920 was annotated as the small heat shock protein HSP20 in sandalwood. Sal1G00910 was annotated as a hypothetical protein of sandalwood. Sal4G10880 was annotated as a homeobox-leucine zipper protein (ATHB-15) in sandalwood. In this study, a cDNA library of sandalwood was successfully constructed using a yeast one-hybrid technique, and the transcription factors that might interact with SaSSY gene promoters were screened. This study provides a foundation for exploring the molecular regulatory mechanism involved in the formation of sandalwood heartwood.

Nudix hydrolase WvNUDX24 is involved in borneol biosynthesis in Wurfbainia villosa

Borneol, camphor, and bornyl acetate are highly promising monoterpenoids widely used in medicine, flavor, food, and chemical applications. Bornyl diphosphate (BPP) serves as a common precursor for the biosynthesis of these monoterpenoids. Although bornyl diphosphate synthase (BPPS) that catalyzes the cyclization of geranyl diphosphate (GPP) to BPP has been identified in multiple plants, the enzyme responsible for the hydrolysis of BPP to produce borneol has not been reported. Here, we conducted in vitro and in vivo functional characterization to identify the Nudix hydrolase WvNUDX24 from W. villosa, which specifically catalyzes the hydrolysis of BPP to generate bornyl phosphate (BP), and then BP forms borneol under the action of phosphatase. Subcellular localization experiments indicated that the hydrolysis of BPP likely occurs in the cytoplasm. Furthermore, site-directed mutagenesis experiments revealed that four critical residues (R84, S96, P98, and G99) for the hydrolysis activity of WvNUDX24. Additionally, the functional identification of phosphatidic acid phosphatase (PAP) demonstrated that WvPAP5 and WvPAP10 were able to hydrolyze geranylgeranyl diphosphate (GGPP) and farnesyl diphosphate (FPP) to generate geranylgeranyl phosphate (GGP) and farnesyl phosphate (FP), respectively, but could not hydrolyze BPP, GPP, and neryl diphosphate (NPP) to produce corresponding monophosphate products. These findings highlight the essential role of WvNUDX24 in the first step of BPP hydrolysis to produce borneol and provide genetic elements for the production of BPP-related terpenoids through plant metabolic engineering and synthetic biology.

Comparative physiological, biochemical, metabolomic, and transcriptomic analyses reveal the formation mechanism of heartwood for Acacia melanoxylon

Acacia melanoxylon is well known as a valuable commercial tree species owing to its high-quality heartwood (HW) products. However, the metabolism and regulatory mechanism of heartwood during wood development remain largely unclear. In this study, both microscopic observation and content determination proved that total amount of starches decreased and phenolics and flavonoids increased gradually from sapwood (SW) to HW. We also obtained the metabolite profiles of 10 metabolites related to phenolics and flavonoids during HW formation by metabolomics. Additionally, we collected a comprehensive overview of genes associated with the biosynthesis of sugars, terpenoids, phenolics, and flavonoids using RNA-seq. A total of ninety-one genes related to HW formation were identified. The transcripts related to plant hormones, programmed cell death (PCD), and dehydration were increased in transition zone (TZ) than in SW. The results of RT-PCR showed that the relative expression level of genes and transcription factors was also high in the TZ, regardless of the horizontal or vertical direction of the trunk. Therefore, the HW formation took place in the TZ for A. melanoxylon from molecular level, and potentially connected to plant hormones, PCD, and cell dehydration. Besides, the increased expression of sugar and terpenoid biosynthesis-related genes in TZ further confirmed the close connection between terpenoid biosynthesis and carbohydrate metabolites of A. melanoxylon. Furthermore, the integrated analysis of metabolism data and RNA-seq data showed the key transcription factors (TFs) regulating flavonoids and phenolics accumulation in HW, including negative correlation TFs (WRKY, MYB) and positive correlation TFs (AP2, bZIP, CBF, PB1, and TCP). And, the genes and metabolites from phenylpropanoid and flavonoid metabolism and biosynthesis were up-regulated and largely accumulated in TZ and HW, respectively. The findings of this research provide a basis for comprehending the buildup of metabolites and the molecular regulatory processes of HW formation in A. melanoxylon.

Improved chromosome-level genome assembly of Indian sandalwood (Santalum album)

Santalum album is a well-known aromatic and medicinal plant that is highly valued for the essential oil (EO) extracted from its heartwood. In this study, we present a high-quality chromosome-level genome assembly of S. album after integrating PacBio Sequel, Illumina HiSeq paired-end and high-throughput chromosome conformation capture sequencing technologies. The assembled genome size is 207.39 M with a contig N50 of 7.33 M and scaffold N50 size of 18.31 M. Compared with three previously published sandalwood genomes, the N50 length of the genome assembly was longer. In total, 94.26% of the assembly was assigned to 10 pseudo-chromosomes, and the anchor rate far exceeded that of a recently released value. BUSCO analysis yielded a completeness score of 94.91%. In addition, we predicted 23,283 protein-coding genes, 89.68% of which were functionally annotated. This high-quality genome will provide a foundation for sandalwood functional genomics studies, and also for elucidating the genetic basis of EO biosynthesis in S. album.

Environmental factors influencing potential distribution of Schisandra sphenanthera and its accumulation of medicinal components

Schisandrae Sphenantherae Fructus (SSF), the dry ripe fruit of Schisandra sphenanthera Rehd. et Wils., is a traditional Chinese medicine with wide application potential. The quality of SSF indicated by the composition and contents of secondary metabolites is closely related to environmental factors, such as regional climate and soil conditions. The aims of this study were to predict the distribution patterns of potentially suitable areas for S. sphenanthera in China and pinpoint the major environmental factors influencing its accumulation of medicinal components. An optimized maximum entropy model was developed and applied under current and future climate scenarios (SSP1-RCP2.6, SSP3-RCP7, and SSP5-RCP8.5). Results show that the total suitable areas for S. sphenanthera (179.58×104 km2) cover 18.71% of China's territory under the current climatic conditions (1981-2010). Poorly, moderately, and highly suitable areas are 119.00×104 km2, 49.61×104 km2, and 10.98×104 km2, respectively. The potentially suitable areas for S. sphenanthera are predicted to shrink and shift westward under the future climatic conditions (2041-2070 and 2071-2100). The areas of low climate impact are located in southern Shaanxi, northwestern Guizhou, southeastern Chongqing, and western Hubei Provinces (or Municipality), which exhibit stable and high suitability under different climate scenarios. The contents of volatile oils, lignans, and polysaccharides in SSF are correlated with various environmental factors. The accumulation of major secondary metabolites is primarily influenced by temperature variation, seasonal precipitation, and annual precipitation. This study depicts the potential distribution of S. sphenanthera in China and its spatial change in the future. Our findings decipher the influence of habitat environment on the geographical distribution and medicinal quality of S. sphenanthera, which could have great implications for natural resource conservation and artificial cultivation.

Characterization of sandalwood (E,E)-α-farnesene synthase whose overexpression enhances cold tolerance through jasmonic acid biosynthesis and signaling in Arabidopsis

MAIN CONCLUSION

Santalum album (E,E)-α-farnesene synthase catalyzes FPP into (E,E)-α-farnesene. Overexpression of the SaAFS gene positively improved cold stress tolerance through JA biosynthesis and signaling pathways in Arabidopsis. Volatile terpenoids are released from plants that suffer negative effects following exposure to various biotic and abiotic stresses. Recent studies revealed that (E,E)-α-farnesene synthase (AFS) plays a significant role in a plant's defence against biotic attack. However, little is known about whether AFS contributes to plant resistance to cold stress. In this study, a SaAFS gene was isolated from Indian sandalwood (Santalum album L.) and functionally characterized. The SaAFS protein mainly converts farnesyl diphosphate to (E,E)-α-farnesene. SaAFS was clustered into the AFS clade from angiosperms, suggesting a highly conserved enzyme. SaAFS displayed a significant response to cold stress and methyl jasmonate. SaAFS overexpression (OE) in Arabidopsis enhanced cold tolerance by increasing proline content, reducing malondialdehyde content, electrolyte leakage, and accumulating reactive oxygen species. Transcriptomic analysis revealed that upregulated genes related to stress response and JA biosynthesis and signaling were detected in SaAFS-OE lines compared with wild type plants that were exposed to cold stress. Endogenous JA and jasmonoyl-isoleucine content increased significantly in SaAFS-OE lines exposed to cold stress. Collectively considered, these results suggest that the SaAFS gene is a positive regulator during cold stress tolerance via JA biosynthesis and signaling pathways.

Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Sandalwood is one of the most expensive woods in the world and is well known for its long-lasting and distinctive aroma. In our study, chromosome-level genome assemblies for two sandalwood species (Santalum album and Santalum yasi) were constructed by integrating NGS short reads, RNA-seq, and Hi-C libraries with PacBio HiFi long reads. The S. album and S. yasi genomes were both assembled into 10 pseudochromosomes with a length of 229.59 Mb and 232.64 Mb, containing 21,673 and 22,816 predicted genes and a repeat content of 28.93% and 29.54% of the total genomes, respectively. Further analyses resolved a Santalum-specific whole-genome triplication event after divergence from ancestors of the Santalales lineage Malania, yet due to dramatic differences in transposon content, the Santalum genomes were only one-sixth the size of the Malania oleifera genome. Examination of RNA-seq data revealed a suite of genes that are differentially expressed in haustoria and might be involved in host hemiparasite interactions. The two genomes presented here not only provide an important comparative dataset for studying genome evolution in early diverging eudicots and hemiparasitic plants but will also hasten the application of conservation genomics for a lineage of trees recovering from decades of overexploitation.

Comparative Genome-Wide Analysis of Two Caryopteris x Clandonensis Cultivars: Insights on the Biosynthesis of Volatile Terpenoids

Caryopteris x Clandonensis, also known as bluebeard, is an ornamental plant containing a large variety of terpenes and terpene-like compounds. Four different cultivars were subjected to a principal component analysis to elucidate variations in terpenoid-biosynthesis and consequently, two representative cultivars were sequenced on a genomic level. Functional annotation of genes as well as comparative genome analysis on long read datasets enabled the identification of cultivar-specific terpene synthase and cytochrome p450 enzyme sequences. This enables new insights, especially since terpenoids in research and industry are gaining increasing interest due to their importance in areas such as food preservation, fragrances, or as active ingredients in pharmaceutical formulations. According to BUSCO assessments, the presented genomes have an average size of 355 Mb and about 96.8% completeness. An average of 52,090 genes could be annotated as putative proteins, whereas about 42 were associated with terpene synthases and about 1340 with cytochrome p450 enzymes.

Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings

Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.

Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses

Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.

Evaluation of larvicidal enhanced activity of sandalwood oil via nano-emulsion against Culex pipiens and Ades aegypti

Mosquito control with essential oils is a trending strategy using aqueous oil nano-emulsions to expand their performance. Sandalwood essential oil and its prepared nano-emulsion used to estimate their larvicidal activities against the 3rd instar larvae of Culex pipiens and Aedes aegypti and their effects on larval tissue detoxifying enzymes. Sandalwood nano-emulsion was characterized by homogeneous, stable, average particles size (195.7 nm), polydispersity index (0.342), and zeta potential (−20.1 mV). Morphologically showed a regular spherical shape in size ranged from 112 to 169 nm that confirmed via scanning electron microscopy. Oil analysis identified sesquiterpene alcohols, mainly santalols, terpenoids, aromatic compounds, fatty acid methyl esters, and phenolic compounds. Larvicidal activities of the oil and its nano-emulsion indicated dose, formulation, and exposure time-related mortality after 24 and 48 h in both species. After 24 h, 100% mortality was detected at 1000 ppm for the nano-emulsion with LC₅₀ of 187.23 and 232.18 ppm and at 1500 ppm for the essential oil with an LC₅₀ of 299.47 and 349.59 ppm against the 3rd larvae Cx. pipiens and Ae. aegypti, respectively. Meanwhile, an enhanced significant effect of the nano-emulsion was observed compared to oil exposure in decreasing total protein content and the activities of alkaline phosphatase and β-esterase enzymes, and increasing α-esterase and glutathione S-transferase activities in larval body tissues. Results demonstrated the enhanced larvicidal potential of sandalwood oil nano-emulsion over that of oil. The effect involved alterations in the detoxifying enzymes based on the existing natural active ingredients against Cx. pipiens and Ae. aegypti larvae.

Engineering plant family TPS into cyanobacterial host for terpenoids production

Terpenoids are synthesized naturally by plants as secondary metabolites, and are diverse and complex in structure with multiple applications in bioenergy, food, cosmetics, and medicine. This makes the production of terpenoids such as isoprene, β-phellandrene, farnesene, amorphadiene, and squalene valuable, owing to which their industrial demand cannot be fulfilled exclusively by plant sources. They are synthesized via the Methylerythritol phosphate pathway (MEP) and the Mevalonate pathway (MVA), both existing in plants. The advent of genetic engineering and the latest accomplishments in synthetic biology and metabolic engineering allow microbial synthesis of terpenoids. Cyanobacteria manifest to be the promising hosts for this, utilizing sunlight and CO2. Cyanobacteria possess MEP pathway to generate precursors for terpenoid synthesis. The terpenoid synthesis can be amplified by overexpressing the MEP pathway and engineering MVA pathway genes. According to the desired terpenoid, terpene synthases unique to the plant kingdom must be incorporated in cyanobacteria. Engineering an organism to be used as a cell factory comes with drawbacks such as hampered cell growth and disturbance in metabolic flux. This review set forth a comparison between MEP and MVA pathways, strategies to overexpress these pathways with their challenges.

Metabolic Engineering of Saccharomyces cerevisiae for Production of Fragrant Terpenoids from Agarwood and Sandalwood

Sandalwood and agarwood essential oils are rare natural oils comprising fragrant terpenoids that have been used in perfumes and incense for millennia. Increasing demand for these terpenoids, coupled with difficulties in isolating them from natural sources, have led to an interest in finding alternative production platforms. Here, we engineered the budding yeast Saccharomyces cerevisiae to produce fragrant terpenoids from sandalwood and agarwood. Specifically, we constructed strain FPPY005_39850, which overexpresses all eight genes in the mevalonate pathway. Using this engineered strain as the background strain, we screened seven distinct terpene synthases from agarwood, sandalwood, and related plant species for their activities in the context of yeast. Five terpene synthases led to the production of fragrant terpenoids, including α-santalene, α-humulene, δ-guaiene, α-guaiene, and β-eudesmol. To our knowledge, this is the first demonstration of β-eudesmol production in yeast. We further improved the production titers by downregulating ERG9, a key enzyme from a competing pathway, as well as employing enzyme fusions. Our final engineered strains produced fragrant terpenoids at up to 101.7 ± 6.9 mg/L. We envision our work will pave the way for a scalable route to these fragrant terpenoids and further establish S. cerevisiae as a versatile production platform for high-value chemicals.

Identification and Functional Analysis of SabHLHs in Santalum album L

Santalum album L., a semi-parasitic evergreen tree, contains economically important essential oil, rich in sesquiterpenoids, such as (Z) α- and (Z) β-santalol. However, their transcriptional regulations are not clear. Several studies of other plants have shown that basic-helix-loop-helix (bHLH) transcription factors (TFs) were involved in participating in the biosynthesis of sesquiterpene synthase genes. Herein, bHLH TF genes with similar expression patterns and high expression levels were screened by co-expression analysis, and their full-length ORFs were obtained. These bHLH TFs were named SaMYC1, SaMYC3, SaMYC4, SaMYC5, SabHLH1, SabHLH2, SabHLH3, and SabHLH4. All eight TFs had highly conserved bHLH domains and SaMYC1, SaMYC3, SaMYC4, and SaMYC5, also had highly conserved MYC domains. It was indicated that the eight genes belonged to six subfamilies of the bHLH TF family. Among them, SaMYC1 was found in both the nucleus and the cytoplasm, while SaMYC4 was only localized in the cytoplasm and the remaining six TFs were localized in nucleus. In a yeast one-hybrid experiment, we constructed decoy vectors pAbAi-SSy1G-box, pAbAi-CYP2G-box, pAbAi-CYP3G-box, and pAbAi-CYP4G-box, which had been transformed into yeast. We also constructed pGADT7-SaMYC1 and pGADT7-SabHLH1 capture vectors and transformed them into bait strains. Our results showed that SaMYC1 could bind to the G-box of SaSSy, and the SaCYP736A167 promoter, which SaSSy proved has acted as a key enzyme in the synthesis of santalol sesquiterpenes and SaCYP450 catalyzed the ligation of santalol sesquiterpenes into terpene. We have also constructed pGreenII 62-SK-SaMYC1, pGreenII 0800-LUC-SaSSy and pGreenII 0800-LUC-SaCYP736A167 via dual-luciferase fusion expression vectors and transformed them into Nicotiana benthamiana using an Agrobacterium-mediated method. The results showed that SaMYC1 was successfully combined with SaSSy or SaCYP736A167 promoter and the LUC/REN value was 1.85- or 1.55-fold higher, respectively, than that of the control group. Therefore, we inferred that SaMYC1 could activate both SaSSy and SaCYP736A167 promoters.

Advances in Understanding Silicon Transporters and the Benefits to Silicon-Associated Disease Resistance in Plants

Silicon (Si) is the second most abundant element after oxygen in the earth’s crust and soil. It is available for plant growth and development, and it is considered as quasi-essential for plant growth. The uptake and transport of Si is mediated by Si transporters. With the study of the molecular mechanism of Si uptake and transport in higher plants, different proteins and coding genes with different characteristics have been identified in numerous plants. Therefore, the accumulation, uptake and transport mechanisms of Si in various plants appear to be quite different. Many studies have reported that Si is beneficial for plant survival when challenged by disease, and it can also enhance plant resistance to pathogens, even at low Si accumulation levels. In this review, we discuss the distribution of Si in plants, as well as Si uptake, transport and accumulation, with a focus on recent advances in the study of Si transporters in different plants and the beneficial roles of Si in disease resistance. Finally, the application prospects are reviewed, leading to an exploration of the benefits of Si uptake for plant resistance against pathogens.

Transcriptomics analysis of field-droughted pear (Pyrus spp.) reveals potential drought stress genes and metabolic pathways

Drought acts as a major abiotic stress that hinders plant growth and crop productivity. It is critical, as such, to discern the molecular response of plants to drought in order to enhance agricultural yields under droughts as they occur with increasing frequency. Pear trees are among the most crucial deciduous fruit trees worldwide, and yet the molecular mechanisms of drought tolerance in field-grown pear remain unclear. In this study, we analyzed the differences in transcriptome profiles of pear leaves, branches, and young fruits in irrigation vs field-drought conditions over the growing seasons. In total, 819 differentially expressed genes (DEGs) controlling drought response were identified, among which 427 DEGs were upregulated and 392 DEGs were downregulated. Drought responsive genes were enriched significantly in monoterpenoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis. Fourteen phenylpropanoid, five flavonoid, and four monoterpenoid structural genes were modulated by field drought stress, thereby indicating the transcriptional regulation of these metabolic pathways in fruit exposed to drought. A total of 4,438 transcription factors (TFs) belonging to 30 TF families were differentially expressed between drought and irrigation, and such findings signal valuable information on transcriptome changes in response to drought. Our study revealed that pear trees react to drought by modulating several secondary metabolic pathways, particularly by stimulating the production of phenylpropanoids as well as volatile organic compounds like monoterpenes. Our findings are of practical importance for agricultural breeding programs, while the resulting data is a resource for improving drought tolerance through genetic engineering of non-model, but economically important, perennial plants.

Diversity and Functional Evolution of Terpene Synthases in Rosaceae

Terpenes are organic compounds and play important roles in plant development and stress response. Terpene synthases (TPSs) are the key enzymes for the biosynthesis of terpenes. For Rosaceae species, terpene composition represents a critical quality attribute, but limited information is available regarding the evolution and expansion occurring in the terpene synthases gene family. Here, we selected eight Rosaceae species with sequenced and annotated genomes for the identification of TPSs, including three Prunoideae, three Maloideae, and two Rosoideae species. Our data showed that the TPS gene family in the Rosaceae species displayed a diversity of family numbers and functions among different subfamilies. Lineage and species-specific expansion of the TPSs accompanied by frequent domain loss was widely observed within different TPS clades, which might have contributed to speciation or environmental adaptation in Rosaceae. In contrast to Maloideae and Rosoideae species, Prunoideae species owned less TPSs, with the evolution of Prunoideae species, TPSs were expanded in modern peach. Both tandem and segmental duplication significantly contributed to TPSs expansion. Ka/Ks calculations revealed that TPSs genes mainly evolved under purifying selection except for several pairs, where the divergent time indicated TPS-e clade was diverged relatively anciently. Gene function classification of TPSs further demonstrated the function diversity among clades and species. Moreover, based on already published RNA-Seq data from NCBI, the expression of most TPSs in Malus domestica, Prunus persica, and Fragaria vesca displayed tissue specificity and distinct expression patterns either in tissues or expression abundance between species and TPS clades. Certain putative TPS-like proteins lacking both domains were detected to be highly expressed, indicating the underlying functional or regulatory potentials. The result provided insight into the TPS family evolution and genetic information that would help to improve Rosaceae species quality.

Transcriptomics of tapping and healing process in frankincense tree during resin production

Frankincense tree (Boswellia sacra Fluek) has been poorly known on how it responds to tapping and wound-recovery process at molecular levels. Here, we used RNA-sequencing analysis to profile transcriptome of B. sacra after 30 min, 3 h and 6 h of post-tapping. Results showed 5525 differentially expressed genes (DEGs) that were related to terpenoid biosynthesis, phytohormonal regulation, cellular transport, and cell-wall synthesis. Plant-growth-regulators were applied exogenously which showed regulation of endogenous jasmonates and resulted in rapid recovery of cell-wall integrity by significantly up-regulated gene expression of terpenoid biosynthesis (germacrene-D synthase, B-amyrin synthase, and squalene epioxidase-1) and cell-wall synthesis (xyloglucan endotransglucosylase, cellulose synthase-A, and cell-wall hydrolase) compared to control. These findings suggest that tapping immediately activated several cell-developmental and regeneration processes, alongwith defense-induced terpenoid metabolism, to improve the healing process in epidermis. Exogenous growth regulators, especially jasmonic acid, can drastically help tree recovery from tissue degeneration and might help in tree conservation purposes.

Water deficit stress responses of monoterpenes and sesquiterpenes in different Iranian cultivars of basil

Ocimum basilicum, a popular aromatic plant, contains aromatic terpenes of terpenoids with in vivo and in vitro verified cytotoxicity. Considering the characteristics and potential of its utilization, it would be attractive to reveal its regulation and biosynthesis, originally at the molecular level under water deficit stress. For this aim, for the first time, the gene encoding the enzyme involved in the end step of the MEP biosynthetic pathways (HDR) was cloned, and the accumulation ratio of linalool, germacrene D and γ-cadinene compounds as well as the expression trait of four critical genes (i.e., HDR, LinS, GerS, and GadS) was assessed under water deficit stress in three Iranian cultivars of basil. The highest value of linalool and γ-cadinene were detected for Cultivar 1 (Cult. 1) under mild stress (W1; 52.6 and 21.1%), while insignificant amounts were obtained for Cultivar 3 (Cult. 3). The germacrene D level of Cultivar 2 (Cult. 2) increased under severe and moderate water stresses as compared with mild water deficit stress. Apart from some expectation, all the studied genes demonstrated divergent transcription ratios under water deficit stress. Principal component analyses (PCA) showed that the relative water content (RWC) and HDR gene expression correlated significantly with essential oil components and gene expression in Cult. 1 and 2, which could represent an elevated demand for corresponding metabolites in the plant tissues. The present work elaborates on the regulation of the mentioned genes, and the results indicate that the production of terpenoids might be a drought stress-dependent and cultivar-dependent procedure.

Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus

Linalool and nerolidol are terpene alcohols that occur naturally in many aromatic plants and are commonly used in food and cosmetic industries as flavors and fragrances. In plants, linalool and nerolidol are biosynthesized as a result of respective linalool synthase and nerolidol synthase, or a single linalool/nerolidol synthase. In our previous work, we have isolated a linalool/nerolidol synthase (designated as PamTps1) from a local herbal plant, Plectranthus amboinicus, and successfully demonstrated the production of linalool and nerolidol in an Escherichia coli system. In this work, the biochemical properties of PamTps1 were analyzed, and its 3D homology model with the docking positions of its substrates, geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15) in the active site were constructed. PamTps1 exhibited the highest enzymatic activity at an optimal pH and temperature of 6.5 and 30 °C, respectively, and in the presence of 20 mM magnesium as a cofactor. The Michaelis-Menten constant (Km) and catalytic efficiency (kcat/Km) values of 16.72 ± 1.32 µM and 9.57 × 10-3 µM-1 s-1, respectively, showed that PamTps1 had a higher binding affinity and specificity for GPP instead of FPP as expected for a monoterpene synthase. The PamTps1 exhibits feature of a class I terpene synthase fold that made up of α-helices architecture with N-terminal domain and catalytic C-terminal domain. Nine aromatic residues (W268, Y272, Y299, F371, Y378, Y379, F447, Y517 and Y523) outlined the hydrophobic walls of the active site cavity, whilst residues from the RRx8W motif, RxR motif, H-α1 and J-K loops formed the active site lid that shielded the highly reactive carbocationic intermediates from the solvents. The dual substrates use by PamTps1 was hypothesized to be possible due to the architecture and residues lining the catalytic site that can accommodate larger substrate (FPP) as demonstrated by the protein modelling and docking analysis. This model serves as a first glimpse into the structural insights of the PamTps1 catalytic active site as a multi-substrate linalool/nerolidol synthase.

Cloning and expression analysis of mevalonate kinase and phosphomevalonate kinase genes associated with the MVA pathway in Santalum album

Sandalwood (Santalum album L.) is highly valued for its fragrant heartwood and extracted oil. Santalols, which are the main components of that oil, are terpenoids, and these are biosynthesized via the mevalonic acid (MVA) pathway. Mevalonate kinase (MK) and phosphomevalonate kinase (PMK) are key enzymes in the MVA pathway. Little is known about the genes that encode MK and PMK in S. album or the mechanism that regulates their expression. To isolate and identify the functional genes involved in santalol biosynthesis in S. album, an MK gene designated as SaMK, and a PMK gene designated as SaPMK, were cloned from S. album. The sequences of these genes were analyzed. A bioinformatics analysis was conducted to assess the homology of SaMK and SaPMK with MK and PMK genes from other plants. The subcellular localization of SaMK and SaPMK proteins was also investigated, as was the functional complementation of SaMK and SaPMK in yeast. Our results show that the full-length cDNA sequences of SaMK and SaPMK were 1409 bp and 1679 bp long, respectively. SaMK contained a 1381 bp open reading frame (ORF) encoding a polypeptide of 460 amino acids and SaPMK contained a 1527 bp ORF encoding a polypeptide of 508 amino acids. SaMK and SaPMK showed high homology with MK and PMK genes of other plant species. Functional complementation of SaMK in a MK-deficient mutant yeast strain YMR208W and SaPMK in a PMK-deficient mutant yeast strain YMR220W confirmed that cloned SaMK and SaPMK cDNA encode a functional MK and PMK, respectively, mediating MVA biosynthesis in yeast. An analysis of tissue expression patterns revealed that SaMK and SaPMK were constitutively expressed in all the tested tissues. SaMK was highly expressed in young leaves but weakly expressed in sapwood. SaPMK was highly expressed in roots and mature leaves, but weakly expressed in young leaves. Induction experiments with several elicitors showed that SaMK and SaPMK expression was upregulated by methyl jasmonate. These results will help to further study the role of MK and PMK genes during santalol biosynthesis in S. album.

Biosynthetic diversity in triterpene cyclization within the Boswellia genus

This review is not intended to describe the triterpenes isolated from the Boswellia genus, since this information has been covered elsewhere. Instead, the aim is to provide insights into the biosynthesis of triterpenes in Boswellia. This genus, which has 24 species, displays fascinating structural diversity and produces a number of medicinally important triterpenes, particularly boswellic acids. Over 300 volatile components have been reported in the essential oil of Boswellia, and more than 100 diterpenes and triterpenes have been isolated from this genus. Given that no triterpene biosynthetic enzymes have yet been isolated from any members of the Boswellia genus, this review will cover the likely biosynthetic pathways as inferred from structures in nature and the probable types of biosynthetic enzymes based on knowledge of triterpene biosynthesis in other plant species. It highlights the importance of frankincense and the factors and threats affecting its production. It covers triterpene biosynthesis in the genus Boswellia, including dammaranes, tirucallic acids, lupanes, oleananes, ursanes and boswellic acids. Strategies for elucidating triterpene biosynthetic pathways in Boswellia are considered. Furthermore, the possible mechanisms behind wound-induced resin synthesis by the tree and related gene expression profiling are covered. In addition, the influence of the environment and the genotype on the biosynthesis of resin and on variations in the compositions and types of resins will also be reviewed.

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.

Functional characterization of an Indian sandalwood (Santalum album L.) dual-localized bifunctional nerolidol/linalool synthase gene involved in stress response

Essential oils extracted from the heartwood of Indian sandalwood (Santalum album L.) contain linalool and nerolidol as minor components. However, nerolidol/linalool synthase (NES/LIS), which produce linalool and nerolidol, have yet to be characterized in sandalwood. Using a transcriptomic-based approach, a terpene synthase gene was screened from unigenes of transcriptome data derived from S. album seedlings exposed to low temperature (4 °C). The enzyme encoded by these complementary DNAs belongs to the TPS-b clade. Recombinant SaNES/LIS is a bifunctional enzyme that can catalyze the formation of (E)-nerolidol from farnesyl diphosphate and linalool from geranyl diphosphate, respectively. Whereas SaNES/LIS was primarily localized in chloroplastids, both as granular fluorescence and as diffuse fluorescence, it was also detected in the cytosol of a limited number of cells. Agrobacterium tumefaciens-mediated transient gene expression in planta produced the same terpene products as those obtained in vitro. Real-time PCR analysis showed the highest expression of SaNES/LIS in fruits, with about a three-fold higher level than in leaves, followed by flowers, heartwood and roots. SaNES/LIS transcripts were differentially activated in different tissues in response to methyl jasmonate, cold, high temperature, strong illumination, and drought stress. Our results provide novel insight into the role of sandalwood terpenoids in response to various environmental stresses.

Cloning, characterization, and functional analysis of acetyl-CoA C-acetyltransferase and 3-hydroxy-3-methylglutaryl-CoA synthase genes in Santalum album

Sandalwood (Santalum album L.) is famous for its unique fragrance derived from the essential oil of heartwood, whose major components are santalols. To understand the mechanism underlying the biosynthesis of santalols, in this study, we cloned two related genes involved in the mevalonate pathway in S. album coding for acetyl-CoA C-acetyl transferase (AACT) and 3-hydroxy-3-methyglutary-CoA synthase (HMGS). These genes were characterized and functionally analyzed, and their expression profiles were also assessed. An AACT gene designated as SaAACT (GenBank accession No. MH018694) and a HMGS gene designated as SaHMGS (GenBank accession No. MH018695) were successfully cloned from S. album. The deduced SaAACT and SaHMGS proteins contain 415 and 470 amino acids, and the corresponding size of their open-reading frames is 1538 bp and 1807 bp, respectively. Phylogenetic trees showed that the SaAACT protein had the closest relationship with AACT from Hevea brasiliensis and the SaHMGS proteins had the highest homology with HMGS from Siraitia grosvenorii. Functional complementation of SaAACT and SaHMGS in a mutant yeast strain deficient in these proteins confirmed that SaAACT and SaHMGS cDNA encodes functional SaAACT and SaHMGS that mediate mevalonate biosynthesis in yeast. Tissue-specific expression analysis revealed that both genes were constitutively expressed in all examined tissues (roots, sapwood, heartwood, young leaves, mature leaves and shoots) of S. album, both genes showing highest expression in roots. After S. album seedlings were treated with 100 μM methyl jasmonate, the expression levels of SaAACT and SaHMGS genes increased, suggesting that these genes were responsive to this elicitor. These studies provide insight that would allow further analysis of the role of genes related to the sandalwood mevalonate pathway in the regulation of biosynthesis of sandalwood terpenoids and a deeper understanding of the molecular mechanism of santalol biosynthesis.

Integration of silicon and secondary metabolites in plants: a significant association in stress tolerance

As sessile organisms, plants are unable to avoid being subjected to environmental stresses that negatively affect their growth and productivity. Instead, they utilize various mechanisms at the morphological, physiological, and biochemical levels to alleviate the deleterious effects of such stresses. Amongst these, secondary metabolites produced by plants represent an important component of the defense system. Secondary metabolites, namely phenolics, terpenes, and nitrogen-containing compounds, have been extensively demonstrated to protect plants against multiple stresses, both biotic (herbivores and pathogenic microorganisms) and abiotic (e.g. drought, salinity, and heavy metals). The regulation of secondary metabolism by beneficial elements such as silicon (Si) is an important topic. Silicon-mediated alleviation of both biotic and abiotic stresses has been well documented in numerous plant species. Recently, many studies have demonstrated the involvement of Si in strengthening stress tolerance through the modulation of secondary metabolism. In this review, we discuss Si-mediated regulation of the synthesis, metabolism, and modification of secondary metabolites that lead to enhanced stress tolerance, with a focus on physiological, biochemical, and molecular aspects. Whilst mechanisms involved in Si-mediated regulation of pathogen resistance via secondary metabolism have been established in plants, they are largely unknown in the case of abiotic stresses, thus leaving an important gap in our current knowledge.

Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species

As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.

Defensive functions of volatile organic compounds and essential oils from northern white-cedar in China

BACKGROUND

Plants are known to emit diverse volatile organic compounds (VOCs), which may function as signaling substances in plant communication with other organisms. Thuja occidentalis, which is widely cultivated throughout China, releases aromatic VOCs into the air in winter and early spring. The relationship of this cultivated plant with its neighboring plants is necessary for the conservation of biodiversity.

RESULTS

(-)-α-thujone (60.34 ± 5.58%) was found to be the major component in VOCs from the Shenyang population. The essential oils (EOs) from the Kunming and Shenyang populations included the major components (-)-α-thujone, fenchone, (+)-β-thujone, and (+)-hibaene, identified using GC-MS analyses. (-)-α-thujone and (+)-hibaene were purified and identified by NMR identification. EOs and (-)-α-thujone exhibited valuable phytotoxic activities against seed germination and seedling growth of the plants Taraxacum mongolicum and Arabidopsis thaliana. Moreover, the EOs displayed potent inhibitory activity against pathogenic fungi of maize, including Fusarium graminearum, Curvularia lunata, and Bipolaris maydis, as well as one human fungal pathogen, Candida albicans. Quantitative analyses revealed high concentrations of (-)-α-thujone in the leaves of T. occidentalis individuals from both the Shenyang and Kunming populations. However, (-)-α-thujone (0.18 ± 0.17 μg/g) was only detected in the rhizosphere soil to a distance of 0.5 m from the plant.

CONCLUSIONS

Taken together, our results suggest that the phytotoxic effects and antifungal activities of the EOs and (-)-α-thujone in T. occidentalis certainly increased the adaptability of this plant to the environment. Nevertheless, low concentrations of released (-)-α-thujone indicated that reasonable distance of T. occidentalis with other plant species will impair the effects of allelochemical of T. occidentalis.

Cloning, functional characterization and expression analysis of LoTPS5 from Lilium 'Siberia'

Lilium 'Siberia' is a perennial herbaceous plant that is commercially significant because of its snowy white floral color and appealing scent which is mainly due to the presence of monoterpenes and benzoids compounds in floral volatile profile. In the current study, LoTPS5 was cloned and functionally characterized. Results revealed that LoTPS5 specifically generates squalene from FPP, whereas no product was produced when it was incubated with GPP or GGPP. The subcellular localization experiment showed that LoTPS5 was located in plastids. Furthermore, LoTPS5 showed its high expression in the leaf followed by petals and sepals of the flower. Moreover, the expression of LoTPS5 gradually increased from the bud stage and peak at the full-bloom stage. Besides, LoTPS5 showed a diurnal circadian rhythmic pattern with a peak in the afternoon (16:00) followed by deep night (24:00) and morning (8:00), respectively. LoTPS5 is highly responsive to mechanical wounding by rapidly elevating its mRNA transcript level. The current study will provide significant information for future studies of terpenoid and squalene biosynthesis in Lilium 'Siberia'.

Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress

Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Hence, knowledge about genes and regulatory elements is essential to strengthen research on N metabolism in this crop. In this study, we analysed transcriptomes (RNA-seq) in potato tissues (shoot, root and stolon) collected from plants grown in aeroponic culture under controlled conditions with varied N supplies i.e. low N (0.2 milli molar N) and high N (4 milli molar N). High quality data ranging between 3.25 to 4.93 Gb per sample were generated using Illumina NextSeq500 that resulted in 83.60-86.50% mapping of the reads to the reference potato genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistically significance (p ≤ 0.05) and up-regulation with ≥ 2 log2 fold change (FC) and down-regulation with ≤ -2 log2 FC values. In shoots, of total 19730 DEGs, 761 up-regulated and 280 down-regulated significant DEGs were identified. Of total 20736 DEGs in roots, 572 (up-regulated) and 292 (down-regulated) were significant DEGs. In stolons, of total 21494 DEG, 688 and 230 DEGs were significantly up-regulated and down-regulated, respectively. Venn diagram analysis showed tissue specific and common genes. The DEGs were functionally assigned with the GO terms, in which molecular function domain was predominant in all the tissues. Further, DEGs were classified into 24 KEGG pathways, in which 5385, 5572 and 5594 DEGs were annotated in shoots, roots and stolons, respectively. The RT-qPCR analysis validated gene expression of RNA-seq data for selected genes. We identified a few potential DEGs responsive to N deficiency in potato such as glutaredoxin, Myb-like DNA-binding protein, WRKY transcription factor 16 and FLOWERING LOCUS T in shoots; high-affinity nitrate transporter, protein phosphatase-2c, glutaredoxin family protein, malate synthase, CLE7, 2-oxoglutarate-dependent dioxygenase and transcription factor in roots; and glucose-6-phosphate/phosphate translocator 2, BTB/POZ domain-containing protein, F-box family protein and aquaporin TIP1;3 in stolons, and many genes of unknown function. Our study highlights that these potential genes play very crucial roles in N stress tolerance, which could be useful in augmenting research on N metabolism in potato.