Salinity stress induces the production of 2-(2-phenylethyl)chromones and regulates novel classes of responsive genes involved in signal transduction in Aquilaria sinensis calli

Identification of O-Methyltransferases Potentially Contributing to the Structural Diversity of 2-(2-Phenylethyl)chromones in Agarwood

2-(2-Phenylethyl)chromones (PECs) are the primary constituents responsible for the promising pharmacological activities and unique fragrance of agarwood. However, the O-methyltransferases (OMTs) involved in the formation of diverse methylated PECs have not been reported. In this study, we identified one Mg2+-dependent caffeoyl-CoA-OMT subfamily enzyme (AsOMT1) and three caffeic acid-OMT subfamily enzymes (AsOMT2-4) from NaCl-treated Aquilaria sinensis calli. AsOMT1 not only converts caffeoyl-CoA to feruloyl-CoA but also performs nonregioselective methylation at either the 6-OH or 7-OH position of 6,7-dihydroxy-PEC. On the other hand, AsOMT2-4 preferentially utilizes PECs as substrates to produce structurally diverse methylated PECs. Additionally, AsOMT2-4 also accepts nonPEC-type substrates such as caffeic acid and apigenin to generate methylated products. Protein structure prediction and site-directed mutagenesis revealed that residues of L313 and I318 in AsOMT3, as well as S292 and F313 in AsOMT4 determine the distinct regioselectivity of these two OMTs toward apigenin. These findings provide important biochemical evidence of the remarkable structural diversity of PECs in agarwood.

Salty treatment increased bioactive compounds accumulation during agarwood development in Aquilaria sinensis trees

To compare the bioactive compounds in agarwood induced by different methods in Aquilaria sinensis(Lour.) Gilg trees, a two dimensional thin layer chromatograph(2D-TLC) combined with effect directive analysis(EDA) was developed. Three antioxidants were found by 2D-TLC-DPPH and further identified as 2-(2-phenylethyl) chromones(PECs) with LC-MS/MS. The 3 antioxidants decreased along agarwood formation and their compositions in drilling induced agarwood differed with those in microbe culture induced agarwood. Further study showed NaCl treatment promoted antioxidants accumulation in agarwood induced by drilling or hot drilling. Hot drilling combined with salty stimulation was most efficient in some chemicals accumulation, which were identified as PECs with antioxidant, tyrosinase or β-glucosidase inhibiting activities by 2D-TLC-EDA-LC-MS/MS. This study provided a 2D-TLC-EDA-LC-MS/MS method for bioactive compounds screen and qualification of agarwood. Based on this method, non-conventional methods were found to accelerate the accumulation of some bioactive PECs in A. sinensis trees.

Molecular evolution and characterization of type III polyketide synthase gene family in Aquilaria sinensis

2-(2-Phenylethyl) chromone (PEC) and its derivatives are markers of agarwood formation and are also related to agarwood quality. However, the biosynthetic and regulatory mechanisms of PECs still remain mysterious. Several studies suggested that type III polyketide synthases (PKSs) contribute to PEC biosynthesis in Aquilaria sinensis. Furthermore, systematic studies on the evolution of PKSs in A. sinensis have rarely been reported. Herein, we comprehensively analyzed PKS genes from 12 plant genomes and characterized the AsPKSs in detail. A unique branch contained only AsPKS members was identified through evolutionary analysis, including AsPKS01 that was previously indicated to participate in PEC biosynthesis. AsPKS07 and AsPKS08, two tandem-duplicated genes of AsPKS01 and lacking orthologous genes in evolutionary models, were selected for their transient expression in the leaves of Nicotiana benthamiana. Subsequently, PECs were detected in the extracts of N. benthamiana leaves, suggesting that AsPKS07 and AsPKS08 promote PEC biosynthesis. The interaction between the promoters of AsPKS07, AsPKS08 and five basic leucine zippers (bZIPs) from the S subfamily indicated that their transcripts could be regulated by these transcription factors (TFs) and might further contribute to PECs biosynthesis in A. sinensis. Our findings provide valuable insights into the molecular evolution of the PKS gene family in A. sinensis and serve as a foundation for advancing PEC production through the bioengineering of gene clusters. Ultimately, this contribution is expected to shed light on the mechanism underlying agarwood formation.

Anatomical, chemical and endophytic fungal diversity of a Qi-Nan clone of Aquilaria sinensis (Lour.) Spreng with different induction times

Recently, some new Qi-Nan clones of Aquilaria sinensis (Lour.) Spreng which intensively produces high-quality agarwood have been identified and propagated through grafting techniques. Previous studies have primarily focused on ordinary A. sinensis and the differences in composition when compared to Qi-Nan and ordinary A. sinensis. There are few studies on the formation mechanism of Qi-Nan agarwood and the dynamic changes in components and endophytic fungi during the induction process. In this paper, the characteristics, chemical composition, and changes in endophytic fungi of Qi-Nan agarwood induced after 1 year, 2 years, and 3 years were studied, and Qi-Nan white wood was used as the control. The results showed that the yield of Qi-Nan agarwood continued to increase with the induction time over a period of 3 years, while the content of alcohol extract from Qi-Nan agarwood reached its peak at two years. During the formation of agarwood, starch and soluble sugars in xylem rays and interxylary phloem are consumed and reduced. Most of the oily substances in agarwood were filled in xylem ray cells and interxylary phloem, and a small amount was filled in xylem vessels. The main components of Qi-Nan agarwood are also chromones and sesquiterpenes. With an increasing induction time, the content of sesquiterpenes increased, while the content of chromones decreased. The most abundant chromones in Qi-Nan agarwood were 2-(2-Phenethyl) chromone, 2-[2-(3-Methoxy-4-hydroxyphenyl) ethyl] chromone, and2-[2-(4-Methoxyphenyl) ethyl] chromone. Significant differences were observed in the species of the endophytic fungi found in Qi-Nan agarwood at different induction times. A total of 4 phyla, 73 orders, and 448 genera were found in Qi-Nan agarwood dominated by Ascomycota and Basidiomycota. Different induction times had a significant effect on the diversity of the endophytic fungal community in Qi-Nan. After the induction of agarwood formation, the diversity of Qi-Nan endophytic fungi decreased. Correlation analysis showed that there was a significant positive correlation between endophytic fungi and the yield, alcohol extract content, sesquiterpene content, and chromone content of Qi-Nan agarwood, which indicated that endophytic fungi play a role in promoting the formation of Qi-Nan agarwood. Qi-Nan agarwood produced at different induction times exhibited strong antioxidant capacity. DPPH free radical scavenging activity and reactive oxygen species clearance activity were significantly positively correlated with the content of sesquiterpenes and chromones in Qi-Nan agarwood.

Characteristic quality analysis for biologically induced agarwood columns in Aquilaria sinensis

Current artificial agarwood-inducing techniques yield low quality and quantities of agarwood. On account of unclear agarwood formation mechanism there's still no high-efficiency agarwood inducing method globally spread. In this study, a complete agarwood column was taken out of the live tree trunk at 6 months post-treatment by a novel agarwood-inducing method (Agar-Bit) in cultivated Aquilaria sinensis trees, and was first divided into 8 parts (A1-4, B1-4) involving agarwood layer (A part) and brown inner layer (B part) according to its color and length for analysis. These eight parts were analyzed microscope observation, 6 chromones' contents and characteristic chromatograms by HPLC (high performance liquid chromatography), GC-MS (gas chromatography-mass spectrometer) with to determine chemical changes. Other quality characteristics, TLC (thin-layer chromatography) and alcohol soluble extraction content, were also determined. Our results showed that resin changed with A to B part and microstructure changed with length. Six chromones in the eight parts varied with layers. Result of characteristic chromatograms showed that both A and B parts contained six characteristic peaks. Volatile component distributed mainly in A part, but important chromones were also detected in B parts. Results from TLC and alcohol soluble extraction content also showed that B part contained characteristic compounds of agarwood. In addition, some compounds in the essential oil detected by GC-MS in A part produced by Agar-Bit were similar to that found in natural agarwood, compounds in B parts were similar to BC agarwood, as were the results for the TLC and alcohol soluble extraction content. In conclusion, the chemical distribution obtained here from Agar-Bit could provide some clues to optimize high production and high efficiency stimulating method for whole tree full of resin in Aquilaria sinensis and to reveal the subtle agarwood formation mechanism throughout a whole trunk.

Identification of a diarylpentanoid-producing polyketide synthase in the biosynthesis of 2-(2-phenylethyl)chromones in agarwood

Agarwood has been valued as an exquisite, high-grade fragrant wood since ancient times. Due to the scarcity of high-quality agarwood, it is quite expensive, and the number of original plants has been drastically reduced due to overharvesting, including illegal logging. Despite this, a reliable method of agarwood cultivation has yet to be developed. Thus, identifying the biosynthetic pathways of the fragrant components in agarwood might help developers to optimize the culture conditions and create artificial agarwood, by monitoring the expression of the biosynthetic enzymes or their genes. This review presents the characteristics of our recently identified key enzyme, 2-(2-phenylethyl)chromone precursor synthase (PECPS), which generates the common precursor of 2-(2-phenylethyl)chromones (PECs), the main fragrances in agarwood, as well as our reasoning to reach these conclusions. We also discuss the biosynthetic pathway of PECs, unveiled following the identification of PECPS.

RNA-Sequencing Reveals the Involvement of Sesquiterpene Biosynthesis Genes and Transcription Factors during an Early Response to Mechanical Wounding of Aquilaria sinensis

Plants respond to wounding by reprogramming the expression of genes involved in secondary metabolism. Aquilaria trees produce many bioactive secondary metabolites in response to wounding, but the regulatory mechanism of agarwood formation in the early response to mechanical wounding has remained unclear. To gain insights into the process of transcriptome changes and to determine the regulatory networks of Aquilaria sinensis to an early response (15 days) to mechanical wounding, we collected A. sinensis samples from the untreated (Asc1) and treated (Asf1) xylem tissues and performed RNA sequencing (RNA-seq). This generated 49,102,523 (Asc1) and 45,180,981 (Asf1) clean reads, which corresponded to 18,927 (Asc1) and 19,258 (Asf1) genes, respectively. A total of 1596 differentially expressed genes (DEGs) were detected in Asf1 vs. Asc1 (|log2 (fold change)| ≥ 1, Padj ≤ 0.05), of which 1088 were up-regulated and 508 genes were down-regulated. GO and KEGG enrichment analysis of DEGs showed that flavonoid biosynthesis, phenylpropanoid biosynthesis, and sesquiterpenoid and triterpenoid biosynthesis pathways might play important roles in wound-induced agarwood formation. Based on the transcription factor (TF)-gene regulatory network analysis, we inferred that the bHLH TF family could regulate all DEGs encoding for farnesyl diphosphate synthase, sesquiterpene synthase, and 1-deoxy-D-xylulose-5-phosphate synthase (DXS), which contribute to the biosynthesis and accumulation of agarwood sesquiterpenes. This study provides insight into the molecular mechanism regulating agarwood formation in A. sinensis, and will be helpful in selecting candidate genes for improving the yield and quality of agarwood.

Agarwood-The Fragrant Molecules of a Wounded Tree

Agarwood, popularly known as oudh or gaharu, is a fragrant resinous wood of high commercial value, traded worldwide and primarily used for its distinctive fragrance in incense, perfumes, and medicine. This fragrant wood is created when Aquilaria trees are wounded and infected by fungi, producing resin as a defense mechanism. The depletion of natural agarwood caused by overharvesting amidst increasing demand has caused this fragrant defensive resin of endangered Aquilaria to become a rare and valuable commodity. Given that instances of natural infection are quite low, artificial induction, including biological inoculation, is being conducted to induce agarwood formation. A long-term investigation could unravel insights contributing toward Aquilaria being sustainably cultivated. This review will look at the different methods of induction, including physical, chemical, and biological, and compare the production, yield, and quality of such treatments with naturally formed agarwood. Pharmaceutical properties and medicinal benefits of fragrance-associated compounds such as chromones and terpenoids are also discussed.

Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood

2-(2-Phenylethyl)chromones (PECs) are the principal constituents contributing to the distinctive fragrance of agarwood. How PECs are biosynthesized is currently unknown. In this work, we describe a diarylpentanoid-producing polyketide synthase (PECPS) identified from Aquilaria sinensis. Through biotransformation experiments using fluorine-labeled substrate, transient expression of PECPS in Nicotiana benthamiana, and knockdown of PECPS expression in A. sinensis calli, we demonstrate that the C6-C5-C6 scaffold of diarylpentanoid is the common precursor of PECs, and PECPS plays a crucial role in PECs biosynthesis. Crystal structure (1.98 Å) analyses and site-directed mutagenesis reveal that, due to its small active site cavity (247 Å3), PECPS employs a one-pot formation mechanism including a "diketide-CoA intermediate-released" step for the formation of the C6-C5-C6 scaffold. The identification of PECPS, the pivotal enzyme of PECs biosynthesis, provides insight into not only the feasibility of overproduction of pharmaceutically important PECs using metabolic engineering approaches, but also further exploration of how agarwood is formed.

Effects of various artificial agarwood-induction techniques on the metabolome of Aquilaria sinensis

BACKGROUND

Agarwood is a highly sought-after resinous wood for uses in medicine, incense, and perfume production. To overcome challenges associated with agarwood production in Aquilaria sinensis, several artificial agarwood-induction treatments have been developed. However, the effects of these techniques on the metabolome of the treated wood samples are unknown. Therefore, the present study was conducted to evaluate the effects of four treatments: fire drill treatment (F), fire drill + brine treatment (FS), cold drill treatment (D) and cold drill + brine treatment (DS)) on ethanol-extracted oil content and metabolome profiles of treated wood samples from A. sinensis.

RESULTS

The ethanol-extracted oil content obtained from the four treatments differed significantly (F < D < DS < FS). A total of 712 metabolites composed mostly of alkaloids, amino acids and derivatives, flavonoids, lipids, phenolic acids, organic acids, nucleotides and derivatives, and terpenoids were detected. In pairwise comparisons, 302, 155, 271 and 363 differentially accumulated metabolites (DAM) were detected in F_vs_FS, D_vs_DS, F_vs_D and FS_vs_DS, respectively. The DAMs were enriched in flavonoid/flavone and flavonol biosynthesis, sesquiterpenoid and triterpenoid biosynthesis. Generally, addition of brine to either fire or cold drill treatments reduced the abundance of most of the metabolites.

CONCLUSION

The results from this study offer valuable insights into synthetically-induced agarwood production in A. sinensis.

A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis

BACKGROUND

Agarwood, generated from the Aquilaria sinensis, has high economic and medicinal value. Although its genome has been sequenced, the ploidy of A. sinensis paleopolyploid remains unclear. Moreover, the expression changes of genes associated with agarwood formation were not analyzed either.

RESULTS

In the present work, we reanalyzed the genome of A. sinensis and found that it experienced a recent tetraploidization event ~ 63-71 million years ago (Mya). The results also demonstrated that the A. sinensis genome had suffered extensive gene deletion or relocation after the tetraploidization event, and exhibited accelerated evolutionary rates. At the same time, an alignment of homologous genes related to different events of polyploidization and speciation were generated as well, which provides an important comparative genomics resource for Thymelaeaceae and related families. Interestingly, the expression changes of genes related to sesquiterpene synthesis in wounded stems of A. sinensis were also observed. Further analysis demonstrated that polyploidization promotes the functional differentiation of the key genes in the sesquiterpene synthesis pathway.

CONCLUSIONS

By reanalyzing its genome, we found that the tetraploidization event shaped the A. sinensis genome and contributed to the ability of sesquiterpenes synthesis. We hope that these results will facilitate our understanding of the evolution of A. sinensis and the function of genes involved in agarwood formation.

Map of dimorphic switching‑related signaling pathways in Sporothrix schenckii based on its transcriptome

Sporothrix schenckii (S. schenckii) induces sporotrichosis, which has gained attention in recent years due to its worldwide prevalence. The dimorphic switching process is essential for the pathogenesis of S. schenckii. Previously, overexpression of several signal transduction genes, including SsDRK1 and SsSte20, was observed during the mycelium‑to‑yeast transition; these were necessary for asexual development, yeast‑phase cell formation, cell wall integrity and melanin synthesis. However, the mechanisms of the signaling pathways during dimorphic switching of S. schenckii remain unclear. In the present study, transcriptome sequencing of the 48‑h induced yeast forms and mycelium of S. schenckii was performed. In total, 24,904,510 high‑quality clean reads were obtained from mycelium samples and 22,814,406 from 48‑h induced yeast form samples. Following assembly, 31,779 unigene sequences were obtained with 52.98% GC content (The proportion of guanine G and cytosine C to all bases in nucleic acid). The results demonstrated that 12,217 genes, including genes involved in signal transduction and chitin synthesis, were expressed differentially between the two stages. According to these results, a map of the signaling pathways, including two‑component and heterotrimeric G‑protein signaling systems, Ras and MAPK cascades associated with the dimorphic switch, was drawn. Taken together, the transcriptome data and analysis performed in the present study lay the foundation for further research into the molecular mechanisms controlling the dimorphic switch of S. schenckii and support the development of anti‑S. schenckii strategies targeting genes associated with signaling pathways.

Natural products in agarwood and Aquilaria plants: chemistry, biological activities and biosynthesis

Covering: Up to the end of 2019.Agarwood is a resinous portion of Aquilaria trees, which is formed in response to environmental stress factors such as physical injury or microbial attack. It is very sought-after among the natural incenses, as well as for its medicinal properties in traditional Chinese and Ayurvedic medicine. Interestingly, the chemical constituents of agarwood and healthy Aquilaria trees are quite different. Sesquiterpenes and 2-(2-phenethyl)chromones with diverse scaffolds commonly accumulate in agarwood. Similar structures have rarely been reported from the original trees that mainly contain flavonoids, benzophenones, xanthones, lignans, simple phenolic compounds, megastigmanes, diterpenoids, triterpenoids, steroids, alkaloids, etc. This review summarizes the chemical constituents and biological activities both in agarwood and Aquilaria trees, and their biosynthesis is discussed in order to give a comprehensive overview of the research progress on agarwood.

Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud

BACKGROUND

Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown.

RESULTS

The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K+/Na+ ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family.

CONCLUSIONS

Zoysia salt treatment transcriptome shows the 24-h and roots may make significant contributions to the salt tolerance. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation.

Salinity Stress-Mediated Suppression of Expression of Salt Overly Sensitive Signaling Pathway Genes Suggests Negative Regulation by AtbZIP62 Transcription Factor in Arabidopsis thaliana

Salt stress is one of the most serious threats in plants, reducing crop yield and production. The salt overly sensitive (SOS) pathway in plants is a salt-responsive pathway that acts as a janitor of the cell to sweep out Na+ ions. Transcription factors (TFs) are key regulators of expression and/or repression of genes. The basic leucine zipper (bZIP) TF is a large family of TFs regulating various cellular processes in plants. In the current study, we investigated the role of the Arabidopsis thaliana bZIP62 TF in the regulation of SOS signaling pathway by measuring the transcript accumulation of its key genes such as SOS1, 2, and 3, in both wild-type (WT) and atbzip62 knock-out (KO) mutants under salinity stress. We further observed the activation of enzymatic and non-enzymatic antioxidant systems in the wild-type, atbzip62, atcat2 (lacking catalase activity), and atnced3 (lacking 9-cis-epoxycarotenoid dioxygenase involved in the ABA pathway) KO mutants. Our findings revealed that atbzip62 plants exhibited an enhanced salt-sensitive phenotypic response similar to atnced3 and atcat2 compared to WT, 10 days after 150 mM NaCl treatment. Interestingly, the transcriptional levels of SOS1, SOS2, and SOS3 increased significantly over time in the atbzip62 upon NaCl application, while they were downregulated in the wild type. We also measured chlorophyll a and b, pheophytin a and b, total pheophytin, and total carotenoids. We observed that the atbzip62 exhibited an increase in chlorophyll and total carotenoid contents, as well as proline contents, while it exhibited a non-significant increase in catalase activity. Our results suggest that AtbZIP62 negatively regulates the transcriptional events of SOS pathway genes, AtbZIP18 and AtbZIP69 while modulating the antioxidant response to salt tolerance in Arabidopsis.

Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

BACKGROUD

Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information.

FINDINGS

We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18-84.37 million years ago.

CONCLUSIONS

Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.

The Scent of Stress: Evidence From the Unique Fragrance of Agarwood

Agarwood (Aquilaria spp.) fragrance and its origin in stress make it probably the most suitable model to study stress-induced aroma. Production being confined only to certain small pockets of South and Southeast Asia, agarwood is arguably the costliest wood in the world. Formation of fragrant agarwood resin is the outcome of complex biotic, abiotic, and physical stress on the Aquilaria trees. The intricate mechanism by which some 150 odd fragrant molecules that constitute agarwood aroma is formed is still not clearly understood. The present review therefore aims to bring to focus this less known but highly valuable stress-induced aroma from Asia. Discussions on agarwood species, occurrence, distribution, formation, and products have been included as foundation. Although global trade in agarwood and its products is estimated at US$6 billion to US$8 billion, no reliable data are readily available in literature. Therefore, an effort has been made to review the current status of agarwood trade. The element of stress and its correlation to agarwood aroma is discussed in the subsequent sections. Natural agarwood formation as well as technologies and interventions in agarwood induction are stress-based (natural and artificial injury, insect and fungal attack, chemical induction). The molecular triggers are gradually coming to light as new studies are implicating jasmonate, LOX signaling, and other stress reaction routes as the source of agarwood aroma. This review therefore has strived to compile the information that is scattered across scientific as well as other authentic literature and update the reader on the current status. More information about the specific roles of other vital stressors like insects, abiotic, and genetic factors is eagerly awaited from ongoing and future research to further understand the unique fragrance of agarwood.

Time-based LC-MS/MS analysis provides insights into early responses to mechanical wounding, a major trigger to agarwood formation in Aquilaria malaccensis Lam

Mechanical wounding is the major trigger for the formation of agarwood in the tropical tree taxon Aquilaria. To understand the molecular mechanism by which Aquilaria reacts to wounding, we applied a proteomics approach using liquid chromatography electrospray-ionization coupled with tandem mass spectrometry (LC-MS/MS) coupled with bioinformatics analysis and principal component analysis. Protein samples were extracted from wood tissues collected from drilled wounds on the stems of five-year old Aquilaria malaccensis. Samples were collected at different time-points of 0, 2, 6, 12, and 24 h after mechanical wounding for protein identification. Venn diagram analysis showed that 564 out of 2227 identified proteins were time-point specific proteins. GO analysis using the REViGO software (including functional proteins) supported these findings. In total, 20 wound-response proteins and one unknown protein were identified as having important roles in the signaling response to wounding, response to stress, activation of plant defense systems, and plant regeneration. The detected biological processes include brassinosteroid stimulus, polyamine catabolism, hypersensitive response, response to cadmium ions, response to oxidative stress, and malate metabolism, suggesting that the wounded trees must have undergone major plant cell damage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that several wound-response proteins were involved in agarwood formation. Our proteomics data thus provide useful information for understanding the wound response mechanisms that trigger agarwood formation.

Mechanical wounding triggers agarwood synthesis pathways in Aquilaria malaccensis.

Agarwood Induction: Current Developments and Future Perspectives

Agarwood is a resinous part of the non-timber Aquilaria tree, which is a highly valuable product for medicine and fragrance purposes. To protect the endangered Aquilaria species, mass plantation of Aquilaria trees has become a sustainable way in Asian countries to obtain the highly valuable agarwood. As only physiologically triggered Aquilaria tree can produce agarwood, effective induction methods are long sought in the agarwood industry. In this paper, we attempt to provide an overview for the past efforts toward the understanding of agarwood formation, the evolvement of induction methods and their further development prospects by integrating it with high-throughput omics approaches.

Transcriptome analysis reveals complex response of the medicinal/ornamental halophyte Iris halophila Pall. to high environmental salinity

The remediation and subsequent use of saline-alkaline land are of great significance to ecological environment construction and sustainable agricultural development. Iris halophila Pall. is a salt-tolerant medicinal and ornamental plant, which has good application prospects in the ecological construction of saline-alkaline land; therefore, study of the molecular mechanisms of salt tolerance in I. halophila has important theoretical and practical value. To evaluate the molecular mechanism of the response of I. halophila to salt toxicity, I. halophila seedlings were treated with salt (300 mM NaCl) and subjected to deep RNA sequencing. The clean reads were obtained and assembled into 297,188 unigenes. Among them, 1120 and 100 salt-responsive genes were identified in I. halophila shoots and roots, respectively. Among them, the key flavonoid and lignin biosynthetic genes, hormone signaling genes, sodium/potassium ion transporter genes, and transcription factors were analyzed and summarized. Quantitative reverse-transcription PCR analysis strengthened the reliability of the RNA sequencing results. This work provides an overview of the transcriptomic responses to salt toxicity in I. halophila and identifies the responsive genes that may contribute to its reduced salt toxicity. These results lay an important foundation for further study of the molecular mechanisms of salt tolerance in I. halophila and related species.

Molecular cloning and characterization of a novel salt-specific responsive WRKY transcription factor gene IlWRKY2 from the halophyte Iris lactea var. chinensis

Iris lactea var. chinensis is a perennial herbaceous halophyte with high salt tolerance and ornamental value. Previous RNA sequencing analysis revealed a transcription factor gene IlWRKY2 expression was upregulated by salt stress. To obtain the full-length sequence, the basic characteristics of IlWRKY2 and its expression pattern under salt stress. Full-length cDNA of IlWRKY2 was cloned by 3'/5' RACE based on the intermediate sequence obtained by RNA sequencing analysis. Structure analysis of IlWRKY2 were performed by Compute pI/MW tool, PSIPRED and SWISS-MODEL analysis. Sequence analysis of IlWRKY2 were performed by BLAST program, DNAman software, MEGA software and MEME program. IlWRKY2 expression pattern was analyzed by quantitative real-time polymerase chain reaction. The open reading frame of IlWRKY2 is 1338 bp in length, which encodes a protein of 446 amino acids. Amino acid sequence analysis revealed that the IlWRKY2 contains one WRKY domains with a zinc finger motif C-X₅-C-X₂₃-H-X-H. Phylogenetic analysis showed that the IlWRKY2 was much closer to EgWRKY41 from Elaeis guineensis and MaWRKY42 from Musa acuminata subsp. malaccensis. Furthermore, the expression of IlWRKY2 in I. lactea var. chinensis shoots was upregulated by different concentrations of NaCl treatment and increased 16-fold after treatment with 200 mM NaCl for 12 h. Obtained the full-length cDNA of IlWRKY2 which belongs to Group II-b WRKY subfamily. IlWRKY2 expression was obviously induced by salt stress in I. lactea var. chinensis shoots and it may play an important role in halophyte I. lactea var. chinensis adaptation to environmental salt stress.

H2O2 and NADPH oxidases involve in regulation of 2-(2-phenylethyl)chromones accumulation during salt stress in Aquilaria sinensis calli

2-(2-Phenylethyl)chromones are the main compounds responsible for the quality of agarwood, which is widely used in traditional medicines, incenses and perfumes. H₂O₂ and NADPH oxidases (also known as respiratory burst oxidase homologs, Rbohs) mediate diverse physiological and biochemical processes in environmental stress responses. However, little is known about the function of H₂O₂ and NADPH oxidases in 2-(2-phenylethyl)chromones accumulation. In this study, we found that salt stress induced a transient increase in content of H₂O₂ and 2-(2-phenylethyl)chromones accumulation in Aquilaria sinensis calli. Exogenous H₂O₂ remarkably decreased the production of 2-(2-phenylethyl)chromones, while dimethylthiourea (DMTU), a scavenger of H₂O₂, significantly increased 2-(2-phenylethyl)chromones accumulation in salt treated calli. Three new H₂O₂-generating genes, named AsRbohA-C, were isolated and characterized from A. sinensis. Salt stress also induced a transient increase in AsRbohA-C expression and NADPH oxidase activity. Furthermore, exogenous H₂O₂ increased AsRbohA-C expression and NADPH oxidase activity, while DMTU inhibited AsRbohA-C expression and NADPH oxidase activity under salt stress. Moreover, diphenylene iodonium (DPI), the inhibitor of NADPH oxidases, reduced AsRbohA-C expression and NADPH oxidase activity, but significantly induced 2-(2-phenylethyl)chromones accumulation during salt stress. These results clearly demonstrated the central role of H₂O₂ and NADPH oxidases in regulation of salt-induced 2-(2-phenylethyl)chromones accumulation in A. sinensis calli.

Relationship between Expression of Chalcone Synthase Genes and Chromones in Artificial Agarwood induced by Formic Acid Stimulation Combined with Fusarium sp. A2 Inoculation

Agarwood (gaharu) is a fragrant resin produced in the heartwood of resinous Gyrinops and Aquilaria species. Artificial agarwood samples were obtained from Aquilaria sinensis (Lour.) Gilg using formic acid (FA) stimulation combined with Fusarium sp. A2 inoculation. The relationship between the expression of chalcone synthase genes (CHS) and dynamic changes in chromone content was explored in resin-deposited parts of the trunks of A. sinensis. CHS gene expression levels were detected by qRT-PCR analysis. The chemical composition of agarwood obtained from the heartwood of A. sinensis before and within 1 year after induction was determined by GC-MS. After induction with FA stimulation combined with F. sp. A2 inoculation, the CHS1 gene showed relatively high expression, whereas the CHS2 gene showed low expression. The relative gene expression level of CHS1 peaked at 12 months, with a 153.1-fold increase, and the dominant period of the CHS2 gene expression was 10 months with a 14.13-fold increase. Moreover, chromones were not detected until after 2 months, and a large proportion of chromone compounds were detected after 4 months. Chromone content increased with time and peaked at 12 months. CHS1 gene expression was significantly correlated with 6-hydroxy-2-(2-phenylethyl)chromone accumulation, and CHS2 gene expression was significantly correlated with 5-hydroxy-6-methoxy-2-(2-phenylethyl)chromone accumulation. CHS gene expression was extremely sensitive to FA stimulation combined with F. sp. A2 inoculation and responded to late-onset injury. CHS genes expression also preceded the chromone accumulation. This work laid the foundation for studies on the mechanism by which genes regulate chromone biosynthesis pathways during the formation of agarwood resin in A. sinensis.

Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant

BACKGROUND

The ultimate goal of this work was to detect the role of transcription factors (TFs) concordantly expressed with genes related to programmed cell death (PCD) during PCD and salt stress. This work was based on the hypothesis that TFs and their driven genes likely co-express under different stimuli. The conserved superfamily ethylene responsive factor (AP2/ERF) draw attention of the present study as it participates in the response to biotic and abiotic stimuli as well as to program cell death (PCD).

RESULTS

RNA-Seq analysis was done for tobacco (N. benthamiana) leaves exposed to oxalic acid (OA) at 20 mM for 0, 2, 6, 12 and 24 h to induce PCD. Genes up-regulated after 2 h of OA treatment with known function during PCD were utilized as landmarks to select TFs with concordant expression. Knockdown mutants of these TFs were generated in tobacco via virus induced gene silencing (VIGS) in order to detect their roles during PCD. Based on the results of PCD assay, knockout (KO) T-DNA insertion mutants of Arabidopsis as well as over-expression lines of two selected TFs, namely ERF109 and TFIID5, analogs to those in tobacco, were tested under salt stress (0, 100, 150 and 200 mM NaCl).

CONCLUSIONS

Results of knockdown mutant tobacco cells confirmed the influence of these two TFs during PCD. Knockout insertion mutants and over-expression lines indicated the role of ERF109 in conferring salt tolerance in Arabidopsis.