Tissue-specific transcriptome for Rheum tanguticum reveals candidate genes related to the anthraquinones biosynthesis

Identification and characterization of compounds that improve plant photosynthesis and growth under light stress conditions

To meet the escalating food and fuel demands of a growing global population and industry, food production requires a 50% increase by 2050. However, various environmental stresses, such as excessive light, significantly inhibit plant growth and lead to substantial reductions in crop yields. A major contributing factor to such declines is the reduction in photosynthetic capacity. In this study, a chemical-screening system based on standard 96-well plate and tobacco leaf tissue was developed. With this system, several anthraquinone derivatives that could alleviate high light stress from plants were identified. Application of these chemicals induced greater photosynthetic capacities and better plant growth during and after exposure to light stress for 20-96 hours in tobacco, lettuce, tomato and Arabidopsis. Mechanistic investigations unveiled that these chemicals exhibited electron-accepting abilities at PSI in vitro and improve PSI efficiency in vivo, indicating that the photoprotective effect could be a result of PSI acceptor side oxidation induced by these chemicals. Meanwhile, no adverse effects on plant growth were observed in chemical treated plants under non-stressful cultivation conditions. This study implies that anthraquinone derivatives can confer high light stress tolerance in plants, resulting in improved plant photosynthesis and growth in light stress environments.

Tocotrienols in Eleven Species of Hypericum Genus Leaves

Saint John's worts or goatweeds are mostly perennial flowering plants in the Hypericaceae family, formerly under the Clusiaceae family. Teas and macerations of the plants are common in traditional medicines and modern depression and cancer therapies. The most notable bioactive compounds in Hypericum are hyperforin and hypericin. While Hypericum contains a variety of carotenoid and phenolic compounds, which are well documented, there is little available information on tocopherols and almost none on tocotrienols. Considering the frequency of tocotrienol derivatives in Clusiaceae species, this study investigates and reports the presence of tocotrienols in eleven Hypericum species' leaves: H. hircinum, H. hookerianum, H. calycinum, H. xylosteifolium, H. densifolium, H. prolificum, H. kalmianum, H. frondosum, H. olympicum, and two hybrids: H. × moserianum and H × 'Rowallane'. Eight tocopherol and tocotrienol forms (α, β, γ, δ) were detected in the leaves, predominantly containing α-tocopherol. Tocotrienol content was most significant in Myriandra section species and was highest in H. prolificum (22.90 ± 0.63 mg 100 g-1), while the highest tocotrienol proportion was observed in H. × 'Rowallane' (54.12% of total tocochromanols) and H. prolificum (37.27% of total tocochromanols). The results demonstrated significant tocochromanol accumulation in Hypericum leaves.

Dynamic analysis of growth characteristics, secondary metabolites accumulation, and an in-depth understanding of anthraquinones biosynthesis in Rubia cordifolia Linn

Rubia cordifolia is a well-known plant used in oriental medicine plant, and is also serves as the primary traditional source of plant red dyestuffs. With the current depletion of natural resources of R. cordifolia, it is critical to conduct cultivation studies on the R. cordifolia. Here, we report on the dynamic growth characteristics and secondary metabolite accumulation of cultivated R. cordifolia, as well as the discovery of important genes involved in anthraquinone biosynthesis. The results showed that R. cordifolia grows better in sunny environments than in shaded environments, and its triennials better than its biennials, base on the biomass and the concentration of the primary components purpurin and mollugin. The dynamic accumulation of purpurin and mollugin content suggested that 30 June to 15 October is a fair window for harvesting R. cordifolia, and the possibility of a specific transition connection during the purpurin and mollugin biosynthesis process. Furthermore, we sequenced R. cordifolia using SMRT technology for the first time and obtained 45,925 full-length transcripts, 564 alternative splicing events, 3182 transcription factors, 6454 SSRs, and 6361 lncRNAs. We hypothesized an anthraquinone biosynthetic pathway and found 280 full-length transcripts that may be involved in anthraquinone biosynthesis in R. cordifolia. In addition, RT-qPCR was used to detect the relative expression levels of 12 candidate ungenes in the above- and underground parts of R. cordifolia. Above all, our findings have crucial implications for the field management of cultivation and harvesting of cultivated R. cordifolia, and also provide useful genetic information for clarifying the potential genes involved in anthraquinone biosynthesis.

Plant anthraquinones: Classification, distribution, biosynthesis, and regulation

Anthraquinones are polycyclic compounds with an unsaturated diketone structure (quinoid moiety). As important secondary metabolites of plants, anthraquinones play an important role in the response of many biological processes and environmental factors. Anthraquinones are common in the human diet and have a variety of biological activities including anticancer, antibacterial, and antioxidant activities that reduce disease risk. The biological activity of anthraquinones depends on the substitution pattern of their hydroxyl groups on the anthraquinone ring structure. However, there is still a lack of systematic summary on the distribution, classification, and biosynthesis of plant anthraquinones. Therefore, this paper systematically reviews the research progress of the distribution, classification, biosynthesis, and regulation of plant anthraquinones. Additionally, we discuss future opportunities in anthraquinone research, including biotechnology, therapeutic products, and dietary anthraquinones.

Comparative transcriptome analysis and HPLC reveal candidate genes associated with synthesis of bioactive constituents in Rheum palmatum complex

Content of bioactive constituents is one of the most important characteristics in Rheum palmatum complex. Increasing ingredient content through genetic breeding is an effective strategy to solve the contradiction between large market demand and resource depletion, but currently hampered by limited understanding of metabolite biosynthesis in rhubarb. In this study, deep transcriptome sequencing was performed to compare roots, stems, and leaves of two Rheum species (PL and ZK) that show different levels of anthraquinone contents. Approximately 0.52 billion clean reads were assembled into 58,782 unigenes, of which around 80% (46,550) were found to be functionally annotated in public databases. Expression patterns of differential unigenes between PL and ZK were thoroughly investigated in different tissues. This led to the identification of various differentially expressed genes (DEGs) involved in shikimate, MEP, MVA, and polyketide pathways, as well as those involved in catechin and gallic acid biosynthesis. Some structural enzyme genes were shown to be significantly up-regulated in roots of ZK with high anthraquinone content, implying potential central roles in anthraquinone synthesis. Taken together, our study provides insights for future functional studies to unravel the mechanisms underlying metabolite biosynthesis in rhubarb.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01492-z.

A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum

BACKGROUND

Rhubarb is one of common traditional Chinese medicine with a diverse array of therapeutic efficacies. Despite its widespread use, molecular research into rhubarb remains limited, constraining our comprehension of the geoherbalism.

RESULTS

We assembled the genome of Rheum palmatum L., one of the source plants of rhubarb, to elucidate its genome evolution and unpack the biosynthetic pathways of its bioactive compounds using a combination of PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C scaffolding approaches. Around 2.8 Gb genome was obtained after assembly with more than 99.9% sequences anchored to 11 pseudochromosomes (scaffold N50 = 259.19 Mb). Transposable elements (TE) with a continuous expansion of long terminal repeat retrotransposons (LTRs) is predominant in genome size, contributing to the genome expansion of R. palmatum. Totally 30,480 genes were predicted to be protein-coding genes with 473 significantly expanded gene families enriched in diverse pathways associated with high-altitude adaptation for this species. Two successive rounds of whole genome duplication event (WGD) shared by Fagopyrum tataricum and R. palmatum were confirmed. We also identified 54 genes involved in anthraquinone biosynthesis and other 97 genes entangled in flavonoid biosynthesis. Notably, RpALS emerged as a compelling candidate gene for the octaketide biosynthesis after the key residual screening.

CONCLUSION

Overall, our findings offer not only an enhanced understanding of this remarkable medicinal plant but also pave the way for future innovations in its genetic breeding, molecular design, and functional genomic studies.

Transcriptomic divergence of the Rheum palmatum complex derived from top-geoherb and non-geoherb areas provides the insights into geoherbalism properties of rhubarb

Geoherb usually represents high-quality medicinal herbs with better clinical therapeutic effects, and elucidating the geoherbalism is essential for the quality improvement of traditional Chinese Medicine. However, few researches were conducted to clarify the geoherbalism based on a large scale of transcriptomics. In the present study, we compared the transcriptomes of Rheum palmatum complex derived from top-geoherb and non-geoherb areas to show the geoherbalism properties of rhubarb. A total of 412.32 Gb clean reads were obtained with unigene numbers of 100,615 after assembly. Based on the obtained transcriptome datasets, key enzyme-encoding genes involved in the anthraquinones biosynthesis were also obtained. We also found that 21 anthraquinone-related unigenes were differentially expressed between two different groups, and some of these DEGs were correlated to the content accumulation of five free anthraquinones, indicating that the gene expression profiles may promote the geoherbalism formation of rhubarb. In addition, the selective pressure analyses indicated that most paired orthologous genes between these two groups were subject to negative selection, and only a low proportion of orthologs under positive selection were detected. Functional annotation analyses indicated that these positive-selected genes related to the functions such as gene expression, substance transport, stress response and metabolism, indicating that discrepant environment also enhanced the formation of geoherbalism. Our study not only provided insights for the genetic mechanism of geoherbalism of rhubarb, but also laid more genetic cues for the future rhubarb germplasms improvement and utilization.

Recent advances in the identification of biosynthetic genes and gene clusters of the polyketide-derived pathways for anthraquinone biosynthesis and biotechnological applications

Natural anthraquinones are represented by a large group of compounds. Some of them are widespread across the kingdoms, especially in bacteria, fungi and plants, while the others are restricted to certain groups of organisms. Despite the significant pharmacological potential of several anthraquinones (hypericin, skyrin and emodin), their biosynthetic pathways and candidate genes coding for key enzymes have not been experimentally validated. Understanding the genetic and epigenetic regulation of the anthraquinone biosynthetic gene clusters in fungal endophytes would help not only understand their pathways in plants, which ensure their commercial availability, but also favor them as promising systems for prospective biotechnological production.

Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis

Rheum officinale Baill. is an important traditional Chinese medicinal herb, its dried roots and rhizomes being widely utilized to cure diverse diseases. However, previous studies mainly focused on the active compounds and their pharmacological effects, and the molecular mechanism underlying the biosynthesis of these ingredients in R. officinale is still elusive. Here, we performed comparative transcriptome analyses to elucidate the differentially expressed genes (DEGs) in the root, stem, and leaf of R. officinale. A total of 236,031 unigenes with N50 of 769 bp was generated, 136,329 (57.76%) of which were annotated. A total of 5884 DEGs was identified after the comparative analyses of different tissues; 175 and 126 key enzyme genes with tissue-specific expression were found in the anthraquinone, catechin/gallic acid biosynthetic pathway, respectively, and some of these key enzyme genes were verified by qRT-PCR. The phylogeny of the PKS III family in Polygonaceae indicated that probably only PL_741 PKSIII1, PL_11549 PKSIII5, and PL_101745 PKSIII6 encoded PKSIII in the polyketide pathway. These results will shed light on the molecular basis of the tissue-specific accumulation and regulation of secondary metabolites in R. officinale, and lay a foundation for the future genetic diversity, molecular assisted breeding, and germplasm resource improvement of this essential medicinal plant.