Transcriptome-wide identification of the genes responding to replanting disease in Rehmannia glutinosa L. roots

Genome-Wide Identification of the Rehmannia glutinosa miRNA Family and Exploration of Their Expression Characteristics Caused by the Replant Disease Formation-Related Principal Factor

Background/Objectives: Rehmannia glutinosa, a highly valuable medicinal plant in China, is encountering severe replant disease. Replant disease represents a complex stress driven by multiple principal factors (RDFs), including allelochemicals, microbes, and their interactions. miRNAs are recognized as key regulators of plant response to stresses; however, their specific roles within RDFs are not entirely clear. Methods: This study builds six RDF treatments, comprising R. glutinosa continuously planted (SP), normally planted (NP), and NP treated with ferulic acid (FA), Fusarium oxysporum (FO), and a combination of FA with FO (FAFO). sRNA-seq technology was used to identify crucial miRNAs in response to diverse RDFs. Results: In total, 30 sRNA datasets were generated from the SP, NP, FA, FO, and FAFO samples. A total of 160 known and 41 novel miRNAs (RgmiRNAs) were identified in the R. glutinosa genome based on the sRNA database. Abundance analysis revealed that RgmiRNAs in SP exhibited a distinct expression profile in comparison with others. Of these, 124, 86, 86, and 90 RgmiRNAs were differentially expressed in SP, FA, FO, and FAFO compared with NP. Target analysis indicated that RgmiRNAs downregulated in both SP and RDFs impede the organism growth of R. glutinosa. RgmiRNAs upregulated in SP can disrupt root formation and nutrient metabolism, in which, two RgmiR398 were uniquely expressed in SP. It was confirmed to target RgCSD genes. The expression patterns of RgmiR398 and RgCSD indicated that replant disease induces the oxidative damage of R. glutinosa through RgmiR398. Conclusions:RgmiRNA profiling under RDFs provides a theoretical basis for the further clarification of RgmiRNA function in replant disease.

Transcriptome-Wide Identification and Functional Characterization of CIPK Gene Family Members in Actinidia valvata under Salt Stress

Fruit plants are severely constrained by salt stress in the soil due to their sessile nature. Ca2+ sensors, which are known as CBL-interacting protein kinases (CIPKs), transmit abiotic stress signals to plants. Therefore, it is imperative to investigate the molecular regulatory role of CIPKs underlying salt stress tolerance in kiwifruit. In the current study, we have identified 42 CIPK genes from Actinidia. valvata (A.valvata). All the AvCIPKs were divided into four different phylogenetic groups. Moreover, these genes showed different conserved motifs. The expression pattern analysis showed that AvCIPK11 was specifically highly expressed under salt stress. The overexpression of AvCIPK11 in 'Hongyang' (a salt sensitive commercial cultivar from Actinidia chinensis) enhanced salt tolerance by maintaining K+/Na+ homeostasis in the leaf and positively improving the activity of POD. In addition, the salt-related genes AcCBL1 and AcNHX1 had higher expression in overexpression lines. Collectively, our study suggested that AvCIPK11 is involved in the positive regulation of salt tolerance in kiwifruit.

Functional analysis of Rehmannia glutinosa key LRR-RLKs during interaction of root exudates with Fusarium oxysporum reveals the roles of immune proteins in formation of replant disease

Previous studies have indicated that some Rehmannia glutinosa Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are involved in the formation of replant disease. However, it remains unclear how the interaction of LRR-RLKs with a key factor, the interaction between root exudates and Fusarium oxysporum, results in formation of replant disease. In this study, the influences of root exudates, F. oxysporum and the interaction of these two factors on expression of nine R. glutinosa LRR-RLKs (RgLRRs) were analyzed. The resulting eight RgLRRs of them were highly expressed at the early stage, and rapidly declined at later stages under mixed treatment of root exudates and F. oxysporum. The functions of nine RgLRRs under root exudates, F. oxysporum and mixed treatment of root exudates and F. oxysporum were preliminarily analyzed using transient overexpression and RNAi experiments. The results showed that high expression of RgLRR19, RgLRR21, RgLRR23 and RgLRR29 could decrease the damage to root cells from the mixed treatment of root exudates and F. oxysporum, but the interference of these genes enhanced the damage levels of root cells. Based on this, stable transgenic R. glutinosa seedlings were acquired. Overexpression of RgLRR29 conferred resistance of R. glutinosa seedlings to root exudates, F. oxysporum and mixed treatment. These results indicated that the continuous proliferation of F. oxysporum supported by root exudates altered the expression patterns of RgLRRs in R. glutinosa, then disordered the growth and development of R. glutinosa, finally leading to the formation of replant disease.

Integrated Analysis of Physiological, mRNA Sequencing, and miRNA Sequencing Data Reveals a Specific Mechanism for the Response to Continuous Cropping Obstacles in Pogostemon cablin Roots

Pogostemon cablin (patchouli) is a commercially important medicinal and industrial crop grown worldwide for its medicinal and aromatic properties. Patchoulol and pogostone, derived from the essential oil of patchouli, are considered valuable components in the cosmetic and pharmaceutical industries. Due to its high application value in the clinic and industry, the demand for patchouli is constantly growing. Unfortunately, patchouli cultivation has suffered due to severe continuous cropping obstacles, resulting in a significant decline in yield and quality. Moreover, the physiological and transcriptional changes in patchouli in response to continuous cropping obstacles remain unclear. This has greatly restricted the development of the patchouli industry. To explore the mechanism underlying the rapid response of patchouli roots to continuous cropping stress, integrated analysis of the transcriptome and miRNA profiles of patchouli roots under continuous and noncontinuous cropping conditions in different growth periods was conducted using RNA sequencing (RNA-seq) and miRNA-seq and complemented with physiological data. The physiological and biochemical results showed that continuous cropping significantly inhibited root growth, decreased root activity, and increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) and the levels of osmoregulators (malondialdehyde, soluble protein, soluble sugar, and proline). Subsequently, we found 4,238, 3,494, and 7,290 upregulated and 4,176, 3,202, and 8,599 downregulated differentially expressed genes (DEGs) in the three growth periods of continuously cropped patchouli, many of which were associated with primary carbon and nitrogen metabolism, defense responses, secondary metabolite biosynthesis, and transcription factors. Based on miRNA-seq, 927 known miRNAs and 130 novel miRNAs were identified, among which 67 differentially expressed miRNAs (DEMIs) belonging to 24 miRNA families were induced or repressed by continuous cropping. By combining transcriptome and miRNA profiling, we obtained 47 miRNA-target gene pairs, consisting of 18 DEMIs and 43 DEGs, that likely play important roles in the continuous cropping response of patchouli. The information provided in this study will contribute to clarifying the intricate mechanism underlying the patchouli response to continuous cropping obstacles. In addition, the candidate miRNAs and genes can provide a new strategy for breeding continuous cropping-tolerant patchouli.

Key molecular events involved in root exudates-mediated replanted disease of Rehmannia glutinosa

The perennial herbaceous plant, Rehmannia glutinosa Libosch, is one of traditional Chinese medicines with a long history of cultivation. However, replanted disease severely affects its yield and quality in production. In this study, a specific culture device was designed to accurately isolate the root exudates of R. glutinosa. In addition, the formation mechanism of replanted diseases mediated by root exudates was deeply studied in R. glutinosa. The results indicated that root exudates have obvious allelopathic activity, furthermore, metagenomics analysis found that the exudates were found to significantly induce the proliferation of harmful pathogenic fungal and the reduction of probiotics in rhizosphere of R. glutinosa. Further analysis found that, 8,758 genes were differentially expressed in root exudate-treated R. glutinosa plants. These genes mainly involved in critical cellular processes including immune response, hormone metabolism, signaling transduction and cell membrane transport. Of which, numerous genes were found to involve in immune response, such as PR (Pathogenesis-related protein), were highly expressed in root exudate-treated plants. Transiently overexpression experiments found that a PR1 could enhance the resistance of R. glutinosa to root exudates treatment. These results indicated that the interaction between root exudates and microbes altered the expression pattern of the genes related to immune pathway and signaling transduction mediated by it. These disordered genes finally severely affected the growth and development of R. glutinosa, and eventually formed the replanted disease. This study provides a novel approach to collect root exudates and a new data basis for revealing the molecular events occurring in replanted plants.

Physiological and transcriptomic analyses to reveal underlying phenolic acid action in consecutive monoculture problem of Polygonatum odoratum

BACKGROUND

The root rot of fragrant solomonseal (Polygonatum odoratum) has occurred frequently in the traditional P. odoratum cultivating areas in recent years, causing a heavy loss in yield and quality. The phenolic acids in soil, which are the exudates from the P. odoratum root, act as allelochemicals that contribute to the consecutive monoculture problem (CMP) of the medicinal plant. The aim of this study was to get a better understanding of P. odoratum CMP.

RESULTS

The phenolic acid contents, the nutrient chemical contents, and the enzyme activities related to the soil nutrient metabolism in the first cropping (FC) soil and continuous cropping (CC) soil were determined, and the differentially expressed genes (DEGs) related to the regulation of the phenolic acids in roots were analyzed. The results showed that five low-molecule-weight phenolic acids were detected both in the CC soil and FC soil, but the phenolic acid contents in the CC soil were significantly higher than those in the FC soil except vanillic acid. The contents of the available nitrogen, available phosphorus, and available potassium in the CC soil were significantly decreased, and the activities of urease and sucrase in the CC soil were significantly decreased. The genomic analysis showed that the phenolic acid anabolism in P. odoratum in the CC soil was promoted. These results indicated that the phenolic acids were accumulated in the CC soil, the nutrient condition in the CC soil deteriorated, and the nitrogen metabolism and sugar catabolism of the CC soil were lowered. Meantime, the anabolism of phenolic acids was increased in the CC plant.

CONCLUSIONS

The CC system promoted the phenolic acid anabolism in P. odoratum and made phenolic acids accumulate in the soil.

Over-immunity mediated abnormal deposition of lignin arrests the normal enlargement of the root tubers of Rehmannia glutinosa under consecutive monoculture stress

The rapid accumulation of lignin in the cell wall is one of important immune defense mechanism in response to adversity stress in plants. In this study, we found that the enlargement of the root tubers of Rehmannia glutinosa (R. glutinosa) is arrested under consecutive monoculture stress, and this process is accompanied by abnormal accumulation of lignin. Meanwhile, the function of key catalytic enzyme genes in lignin biosynthetic pathway under consecutive monoculture stress was systematically analyzed, of which roles of core genes were validated using reverse genetics. We elucidated that an abnormal deposition of lignin in R. glutinosa roots, induced by consecutive monoculture stress, and arrested the enlargement of root tubers. Additionally, by manipulating the key catalytic enzyme gene RgCCR6, we were able to alter lignin content of roots of R. glutinosa, thereby affecting tuber enlargement. We speculate that cell lignification is an important defense strategy in resistance against consecutive monoculture stress, but the overreacted defense hindered the normal enlargement of root tubers. The findings provide new insights for effectively improving yield reductions of root crops subjected to environmental stress.

Integrated miRNA-mRNA analysis reveals the roles of miRNAs in the replanting benefit of Achyranthes bidentata roots

The yield and quality of the medicinal plant Achyranthes bidentata can be increased when it is replanted into a field cultivated previously with the same crop, however, fundamental aspects of its biology (so-called "replanting benefit") still remain to be elucidated. miRNAs are sRNA molecules involved in the post-transcriptional regulation of gene expression in plant biological processes. Here, 267 conserved and 36 novel miRNAs were identified in A. bidentata roots. We compared the miRNA content of the roots (R1) from first-year planting with that of the roots (R2) of second-year replanting, and screened 21 differentially expressed (DE) miRNAs. Based on in silico functional analysis, integrated miRNA-mRNA datasets allowed the identification of 10 miRNA-target family modules, which might participate in the benefit. The expression profiles of the miRNA-target modules were potentially correlated with the presence of the replanting benefit. The indication was that the miRNA-responsive continuous monoculture could reprogram miRNA-mRNA expression patterns, which possibly promote the root growth and development, enhance its transport activity and strengthen its tolerance to various stresses, thereby improving A. bidentata productivity as observed in the replanting benefit. Our study provides basic data for further research on the molecular mechanisms of the benefit in A. bidentata.

Trends in herbgenomics

From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.

The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.

Differential proteomic analysis of replanted Rehmannia glutinosa roots by iTRAQ reveals molecular mechanisms for formation of replant disease

BACKGROUND

The normal growth of Rehmannia glutinosa, a widely used medicinal plant in China, is severely disturbed by replant disease. The formation of replant disease commonly involves interactions among plants, allelochemicals and microbes; however, these relationships remain largely unclear. As a result, no effective measures are currently available to treat replant disease.

RESULTS

In this study, an integrated R. glutinosa transcriptome was constructed, from which an R. glutinosa protein library was obtained. iTRAQ technology was then used to investigate changes in the proteins in replanted R. glutinosa roots, and the proteins that were expressed in response to replant disease were identified. An integrated R. glutinosa transcriptome from different developmental stages of replanted and normal-growth R. glutinosa produced 65,659 transcripts, which were accurately translated into 47,818 proteins. Using this resource, a set of 189 proteins was found to be significantly differentially expressed between normal-growth and replanted R. glutinosa. Of the proteins that were significantly upregulated in replanted R. glutinosa, most were related to metabolism, immune responses, ROS generation, programmed cell death, ER stress, and lignin synthesis.

CONCLUSIONS

By integrating these key events and the results of previous studies on replant disease formation, a new picture of the damaging mechanisms that cause replant disease stress emerged. Replant disease altered the metabolic balance of R. glutinosa, activated immune defence systems, increased levels of ROS and antioxidant enzymes, and initiated the processes of cell death and senescence in replanted R. glutinosa. Additionally, lignin deposition in R. glutinosa roots that was caused by replanting significantly inhibited tuberous root formation. These key processes provide important insights into the underlying mechanisms leading to the formation of replant disease and also for the subsequent development of new control measures to improve production and quality of replanted plants.

Transcriptome analysis reveals metabolic alteration due to consecutive monoculture and abiotic stress stimuli in Rehamannia glutinosa Libosch

We deeply investigated the mechanism underlying metabolic regulation in response to consecutive monoculture (replanting disease) and different abiotic stresses that unfolded the response mechanism to consecutive monoculture problem through RNA-seq analysis. The consecutive monoculture problem (CMP) resulted of complex environmental stresses mediated by multiple factors. Previous studies have noted that multiple stress factors in consecutive monoculture soils or plants severely limited the interpretation of the critical molecular mechanism, and made a predict that the specifically responding factor was autotoxic allelochemicals. To identify the specifically responding genes, we compared transcriptome changes in roots of Rehamannia glutinosa Libosch using consecutive monoculture, salt, drought, and ferulic acid as stress factors. Comparing with normal growth, 2502, 2672, 2485, and 1956 genes were differentially expressed in R. glutinosa under consecutive monoculture practice, salt, drought, and ferulic acid stress, respectively. In addition, 510 genes were specifically expressed under consecutive monoculture, which were not present under the other stress conditions. Integrating the biological and enrichment analyses of the differentially expressed genes, the result demonstrated that the plants could alter enzyme genes expression to reconstruct the complicated metabolic pathways, which used to tolerate the CMP and abiotic stresses. Furthermore, most of the affected pathway genes were closely related to secondary metabolic processes, and the influence of consecutive monoculture practice on the transcriptome genes expression profile was very similar to the profile under salt stress and then to the profile under drought stress. The outlined schematic diagram unfolded the putative signal regulation mechanism in response to the CMP. Genes that differentially up- or down-regulated under consecutive monoculture practice may play important roles in the CMP or replanting disease in R. glutinosa.

Dynamic transcriptional profiling provides insights into tuberous root development in Rehmannia glutinosa

Rehmannia glutinosa, an herb of the Scrophulariaceae family, is widely cultivated in the Northern part of China. The tuberous root has well-known medicinal properties; however, yield and quality are threatened by abiotic and biotic stresses. Understanding the molecular process of tuberous root development may help identify novel targets for its control. In the present study, we used Illumina sequencing and de novo assembly strategies to obtain a reference transcriptome that is relevant to tuberous root development. We then conducted RNA-seq quantification analysis to determine gene expression profiles of the adventitious root (AR), thickening adventitious root (TAR), and the developing tuberous root (DTR). Expression profiling identified a total of 6794 differentially expressed unigenes during root development. Bioinformatics analysis and gene expression profiling revealed changes in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone biosynthesis during root development. Moreover, we identified and allocated putative functions to the genes involved in tuberous root development, including genes related to major carbohydrate metabolism, hormone metabolism, and transcription regulation. The present study provides the initial description of gene expression profiles of AR, TAR, and DTR, which facilitates identification of genes of interest. Moreover, our work provides insights into the molecular mechanisms underlying tuberous root development and may assist in the design and development of improved breeding schemes for different R. glutinosa varieties through genetic manipulation.