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Plant specialized metabolites (PSMs) play essential roles in the adaptation to harsh environments and function in plant defense responses. PSMs act as key components of defense-related signaling pathways and trigger the extensive expression of defense-related genes. In addition, PSMs serve as antioxidants, participating in the scavenging of rapidly rising reactive oxygen species, and as chelators, participating in the chelation of toxins under stress conditions. PSMs include nitrogen-containing chemical compounds, terpenoids/isoprenoids, and phenolics. Each category of secondary metabolites has a specific biosynthetic pathway, including precursors, intermediates, and end products. The basic biosynthetic pathways of representative PSMs are summarized, providing potential target enzymes of stress-mediated regulation and responses. Multiple metabolic pathways share the same origin, and the common enzymes are frequently to be the targets of metabolic regulation. Most biosynthetic pathways are controlled by different environmental and genetic factors. Here, we summarized the effects of environmental factors, including abiotic and biotic stresses, on PSM biosynthesis in various plants. We also discuss the positive and negative transcription factors involved in various PSM biosynthetic pathways. The potential target genes of the stress-related transcription factors were also summarized. We further found that the downstream targets of these Transcription factors (TFs) are frequently enriched in the synthesis pathway of precursors, suggesting an effective role of precursors in enhancing of terminal products. The present review provides valuable insights regarding screening targets and regulators involved in PSM-mediated plant protection in non-model plants.

Background Plants of the genus Taxus have attracted much attention owing to the natural product taxol, a successful anti-cancer drug. T. fuana and T. yunnanensis are two endangered Taxus species mainly distributed in the Himalayas. In our study, an untargeted metabolomics approach integrated with a targeted UPLC-MS/MS method was applied to examine the metabolic variations between these two Taxus species growing in different environments. Results The level of taxol in T. yunnanensis is much higher than that in T. fuana , indicating a higher economic value of T. yunnanensis for taxol production. A series of specific metabolites, including precursors, intermediates, competitors of taxol, were identified. All the identified intermediates are predominantly accumulated in T. yunnanensis than T. fuana , giving a reasonable explanation for the higher accumulation of taxol in T. yunnanensis . Taxusin and its analogues are highly accumulated in T. fuana , which may consume limited intermediates and block the metabolic flow towards taxol. The contents of total flavonoids and a majority of tested individual flavonoids are significantly accumulated in T. fuana than T. yunnanensis , indicating a stronger environmental adaptiveness of T. fuana . Conclusions Systemic metabolic profiling may provide valuable information for the comprehensive industrial utilization of the germplasm resources of these two endangered Taxus species growing in different environments.

Background Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of Physalis are still controversial. In this study, the complete chloroplast (cp) genomes of four Physalis species ( Physalis angulata , P. alkekengi var. franchetii , P. minima and P. pubescens ) were sequenced, and the first comprehensive cp genome analysis of Physalis was performed, which included the previously published cp genome sequence of Physalis peruviana . Results The Physalis cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the Physalis cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes’ lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced Physalis cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the Physalis cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed Physalis in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value. Conclusion Our results enrich the data on the cp genomes of the genus Physalis . The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of Physalis , and assist in the investigation and utilization of Physalis plants.

Key messageWe employed both metabolomic and transcriptomic approaches to explore the accumulation patterns of physalins, flavonoids and chlorogenic acid in Physalis angulata and revealed the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment.Physalis angulata L. is an annual Solanaceae plant with a number of medicinally active compounds. Despite the potential pharmacological benefits of P. angulata, the scarce genomic information regarding this plant has limited the studies on the mechanisms of bioactive compound biosynthesis. To facilitate the basic understanding of the main chemical constituent biosynthesis pathways, we performed both metabolomic and transcriptomic approaches to reveal the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Untargeted metabolome analysis showed that most physalins, flavonoids and chlorogenic acid were significantly upregulated. Targeted HPLC–MS/MS analysis confirmed variations in the contents of two important representative steroid derivatives (physalins B and G), total flavonoids, neochlorogenic acid, and chlorogenic acid between MeJA-treated plants and controls. Transcript levels of a few steroid biosynthesis-, flavonoid biosynthesis-, and chlorogenic acid biosynthesis-related genes were upregulated, providing a potential explanation for MeJA-induced active ingredient synthesis in P. angulata. Systematic correlation analysis identified a number of novel candidate genes associated with bioactive compound biosynthesis. These results may help to elucidate the regulatory mechanism underlying MeJA-induced active compound accumulation and provide several valuable candidate genes for further functional study.

Background To adapt to constantly changing environments, ancient gymnosperms have coevolved with diverse endophytic fungi that are essential for the fitness and adaptability of the plant host. However, the effect of sex on plant-endophyte interactions in response to environmental stressors remains unknown. RNA-seq integrated with ITS analysis was applied to reveal the potential mechanisms underlying the sex-specific responses of Taxus mairei to ultraviolet (UV)-B radiation. Results Enrichment analysis suggested that sex influenced the expression of several genes related to the oxidation–reduction system, which might play potential roles in sex-mediated responses to UV-B radiations. ITS-seq analysis clarified the effects of UV-B radiation and sex on the composition of endophytic fungal communities. Sex influenced various secondary metabolic pathways, thereby providing chemicals for T. mairei host to produce attractants and/or inhibitors to filter microbial taxa. Analysis of fungal biomarkers suggested that UV-B radiation reduced the effect of sex on fungal communities. Moreover, Guignardia isolate #1 was purified to investigate the role of endophytic fungi in sex-mediated responses to UV-B radiation. Inoculation with spores produced by isolate #1 significantly altered various oxidation–reduction systems of the host by regulating the expression of APX2 , GST7 NCED1 , ZE1 , CS1 , and CM1 . Conclusion These results revealed the roles of endophytic fungi in sex-mediated responses to UV-B radiation and provided novel insights into the sex-specific responses of Taxus trees to environmental stressors. 3pQjBcj-im_YZSujzFCGpb Video Abstract

The flavonoids in the extracts of Ginkgo leaves have been shown to have great medical value: thus, a method to increase the flavonoid contents in these extracts is of significant importance for human health. In the present study, we investigated the changes in flavonoid contents and the corresponding gene expression levels in post-harvest Ginkgo leaves after various treatments. We found that both ultraviolet-B and NaCl treatment induced flavonoid accumulation. However, gene expression analysis showed that the increases in flavonoid contents were achieved by different pathways. Furthermore, post-harvest Ginkgo leaves responded differently to NaCl treatment compared with naturally grown leaves in both flavonoid contents and corresponding gene expression. In addition, combined treatment with ultraviolet-B and NaCl did not further increase the flavonoid contents compared with ultraviolet-B or NaCl treatment alone. Our results indicate the existence of a novel mechanism in response to NaCl treatment in post-harvest Ginkgo leaves, and provide a technique to increase flavonoid content in the pharmaceutical industry.

Physalis macrophysa (PMA) and Physalis ixocarpa (PIX) have significant economic, medicinal, and ornamental value and are often used in the fields of edible fruits, medicinal herbs, and ornamental plants. In the present study, we obtained the complete chloroplast (cp) genome sequences of PMA and PIX, compared to the cp genome sequences of 10 Physalis species, and constructed the phylogenetic tree among the tribe Physaleae. The results showed that the cp genomes of PMA and PIX consisted of a large single copy (LSC) region (87,115 bp and 87,103 bp, respectively), a small single copy (SSC) region (18,412 bp and 18,420 bp, respectively), and a pair of same-length inverted-repeat (IRa and IRb) regions (25,604 bp and 25,674 bp, respectively). The two species contained 132 genes, including 87 encoding proteins, eight encoding ribosomal RNAs (rRNAs), and 37 encoding transfer RNAs (tRNAs), which indicated that the two species have strong similarities with respect to genome structure and gene content. PMA and PIX contained repeat sequences (35 and 40, respectively) and simple-sequence repeats (SSRs) (61 and 60, respectively). Nine regions with considerable nucleotide divergence were found, most of which were located in the LSC and SSC regions. The gene selective pressure analysis indicated that eight genes were affected by positive selection, the Ka/Ks values of which were greater than one. Our phylogenetic results indicated that PMA and PIX had the closest genetic relationship and are closely adjacent to Physalis philadelphica (PPH) in the subtribe Physalinae. Our analysis of the cp genomes in both Physalis species will be beneficial for further research into species identification, phylogeny, evolution, and the potential for germplasm resource exploitation in Physalis.

Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and applied them to evaluate the genetic diversity and population structure of P. angulata. A total of 57 cpSSRs were identified from the chloroplast genome of P. angulata. Among all cpSSR loci, mononucleotide markers were the most abundant (68.24%), followed by tetranucleotide (12.28%), dinucleotide (10.53%), and trinucleotide (8.77%) markers. In total, 30 newly developed cpSSR markers with rich polymorphism and good stability were selected for further genetic diversity and population structure analyses. These cpSSRs amplified a total of 156 alleles, 132 (84.62%) of which were polymorphic. The percentage of polymorphic alleles and the average polymorphic information content (PIC) value of the cpSSRs were 81.29% and 0.830, respectively. Population genetic diversity analysis indicated that the average observed number of alleles (Na), number of effective alleles (He), Nei’s gene diversity (h), and Shannon information indices (I) of 16 P. angulata populations were 1.3161, 1.1754, 0.1023, and 0.1538, respectively. Moreover, unweighted group arithmetic mean, neighbor-joining, principal coordinate, and STRUCTURE analyses indicated that 203 P. angulata individuals from 16 populations were grouped into four clusters. A molecular variance analysis (AMOVA) illustrated the considerable genetic variation among populations, while the gene flow (Nm) value (0.2324) indicated a low level of gene flow among populations. Our study not only provided a batch of efficient genetic markers for research on P. angulata but also laid an important foundation for the protection and genetic breeding of P. angulata resources.

Panax notoginseng (Burk.) F. H. Chen, a species of the genus Panax, radix has been traditionally used to deal with various hematological diseases and cardiovascular diseases since ancient times in East Asia. P. notoginseng produces recalcitrant seeds which are sensitive to desiccation and difficult to store for a long time. However, few data are available on the mechanism of the desiccation sensitivity of P. notoginseng seeds. To gain a comprehensive perspective of the genes associated with desiccation sensitivity, cDNA libraries from seeds under control and desiccation processes were prepared independently for Illumina sequencing. The data generated a total of 70,189,896 reads that were integrated and assembled into 55,097 unigenes with a mean length of 783 bp. In total, 12,025 differentially expressed genes (DEGs) were identified during the desiccation process. Among these DEGs, a number of central metabolism, hormonal network-, fatty acid-, and ascorbate-glutathione-related genes were included. Our data provide a comprehensive resource for identifying the genes associated with the desiccation sensitivity of P. notoginseng seeds.

As a sister genus to Taxus , Pseudotaxus holds significant importance for studying the origin and evolution of the taxane biosynthesis pathway. However, the reference genome of Pseudotaxus chienii is yet unavailable. Here, we report a chromosome-level genome assembly of P. chienii (15.6 Gb). We show that P. chienii only possesses a partial taxane pathway, which terminates before taxane 2α- O -benzoyl transferase (TBT), a crucial enzyme responsible for the production of 10-deacetylbaccatin III. With the emergence of the Taxus genus, the limitation posed by the lacking of functional TBT is overcome, allowing for the extension of the existing taxane biosynthesis pathway into a complete Taxol biosynthesis. The protein structure of metal ion catalysis sites in taxadiene synthase (TS) is conserved across the Pseudotaxus and Taxus genera, providing potential sites for enhancing TS activity through enzyme engineering. This comparative genomic analysis contributes to our understanding of the origin and evolution of taxane biosynthesis within the Taxaceae family. Pseudotaxus is a sister genus to Taxus but lacks a complete taxane biosynthetic pathway. Here, the authors assemble the genome of P. chienii and reveal that the presence of a functional taxane 2α- O -benzoyl transferase in Taxus genus extends the existing taxane biosynthesis pathway into a complete Taxol biosynthesis pathway.