Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress

Integrated PacBio SMRT and Illumina sequencing uncovers transcriptional and physiological responses to drought stress in whole-plant Nitraria tangutorum

Introduction

Nitraria tangutorum Bobr., a prominent xerophytic shrub, exhibits remarkable adaptability to harsh environment and plays a significant part in preventing desertification in northwest China owing to its exceptional drought and salinity tolerance.

Methods

To investigate the drought-resistant mechanism underlying N. tangutorum, we treated 8-week-old seedlings with polyethylene glycol (PEG)-6000 (20%, m/m) to induce drought stress. 27 samples from different tissues (leaves, roots and stems) of N. tangutorum at 0, 6 and 24 h after drought stress treatment were sequenced using PacBio single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing to obtain a comprehensive transcriptome.

Results

The PacBio SMRT sequencing generated 44,829 non-redundant transcripts and provided valuable reference gene information. In leaves, roots and stems, we identified 1162, 2024 and 232 differentially expressed genes (DEGs), respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that plant hormone signaling and mitogen-activated protein kinase (MAPK) cascade played a pivotal role in transmitting stress signals throughout the whole N. tangutorum plant following drought stress. The interconversion of starch and sucrose, as well as the biosynthesis of amino acid and lignin, may represent adaptive strategies employed by N. tangutorum to effectively cope with drought. Transcription factor analysis showed that AP2/ERF-ERF, WRKY, bHLH, NAC and MYB families were mainly involved in the regulation of drought response genes. Furthermore, eight physiological indexes, including content of proline, hydrogen peroxide (H2O2), malondialdehyde (MDA), total amino acid and soluble sugar, and activities of three antioxidant enzymes were all investigate after PEG treatment, elucidating the drought tolerance mechanism from physiological perspective. The weighted gene co-expression network analysis (WGCNA) identified several hub genes serve as key regulator in response to drought through hormone participation, ROS cleavage, glycolysis, TF regulation in N. tangutorum.

Discussion

These findings enlarge genomic resources and facilitate research in the discovery of novel genes research in N. tangutorum, thereby establishing a foundation for investigating the drought resistance mechanism of xerophyte.

Anatomical and Metabolome Features of Haloxylon aphyllum and Haloxylon persicum Elucidate the Resilience against Gall-Forming Insects

Globally, gall-forming insects significantly contribute to the degradation of desert ecosystems. Recent studies have demonstrated that Haloxylon persicum suffers less damage from gall-formers compared to Haloxylon aphyllum. However, the mechanisms driving the long-term metabolic responses of these species to gall-forming biotic stress in their natural environment remain unclear. The current study comparatively analyzes the anatomical features and metabolomic changes in H. aphyllum and H. persicum damaged by gall-forming insects. This research aimed to uncover potential metabolic tolerance mechanisms through GC-MS analysis. The study findings indicate that gall-forming insects cause a reduction in nearly all the anatomical structures of Haloxylon shoots, with the effects being less severe in H. persicum than in H. aphyllum. Thus, the metabolic pathways responsible for the biosynthesis of biologically active substances that enhance resistance to gall inducers were different, specifically in H. aphyllum-the biosynthesis of fatty acids (+their derivatives) and γ-tocopherol (vitamin E) and H. persicum-the biosynthesis of fatty acids (+their derivatives), dialkyl ethers, carbohydrates (+their derivatives), aromatic acid derivatives, phytosterols, γ-tocopherol (vitamin E), phenols, and terpenoids. The results suggest that the modulation of metabolic pathways under biotic stress plays a crucial role in the enhanced survival and growth of H. persicum.

Metabolomic Analysis of the Response of Haloxylon ammodendron and Haloxylon persicum to Drought

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants in arid areas, show strong drought tolerance and environmental adaptability and are therefore ideal model plants for studying the molecular mechanisms of drought tolerance. A metabolomic analysis of H. ammodendron and H. persicum in their natural environment is lacking, and their metabolic response to drought therefore remains unclear. To elucidate the response of H. ammodendron and H. persicum to drought at the metabolic level, a non-targeted metabolomics analysis was carried out herein. Under a dry environment, H. ammodendron exhibited 296 and 252 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively, whereas 452 and 354 DEMs were identified in the positive and negative ion modes in H. persicum, respectively. The results indicated that H. ammodendron responds to drought by increasing the content of organic nitrogen compounds and lignans, neolignans, and related compounds, and reducing the content of alkaloids and derivatives. By contrast, H. persicum adapts to the dry environment by increasing the content of organic acids and their derivatives and reducing the content of lignans, neolignans, and related compounds. In addition, H. ammodendron and H. persicum improved their osmoregulation ability, reactive oxygen species detoxification ability, and cell membrane stability by regulating the key metabolic pathways and anabolism of associated metabolites. This is the first metabolomics report on the response of H. ammodendron and H. persicum to drought in their natural environment, providing a foundation for the further study of their regulatory mechanisms under drought stress.

Transcriptome Profiling of Stem-Differentiating Xylem in Response to Abiotic Stresses Based on Hybrid Sequencing in Cunninghamia lanceolata

Cunninghamia lanceolata (C. lanceolata) belongs to Gymnospermae, which are fast-growing and have desirable wood properties. However, C. lanceolata's stress resistance is little understood. To unravel the physiological and molecular regulation mechanisms under environmental stresses in the typical gymnosperm species of C. lanceolata, three-year-old plants were exposed to simulated drought stress (polyethylene glycol 8000), salicylic acid, and cold treatment at 4 °C for 8 h, 32 h, and 56 h, respectively. Regarding the physiological traits, we observed a decreased protein content and increased peroxidase upon salicylic acid and polyethylene glycol treatment. Superoxide dismutase activity either decreased or increased at first and then returned to normal under the stresses. Regarding the molecular regulation, we used both nanopore direct RNA sequencing and short-read sequencing to reveal a total of 5646 differentially expressed genes in response to different stresses, of which most had functions in lignin catabolism, pectin catabolism, and xylan metabolism, indicating that the development of stem-differentiating xylem was affected upon stress treatment. Finally, we identified a total of 51 AP2/ERF, 29 NAC, and 37 WRKY transcript factors in C. lanceolata. The expression of most of the NAC TFs increased under cold stress, and the expression of most of the WRKY TFs increased under cold and SA stress. These results revealed the transcriptomics responses in C. lanceolata to short-term stresses under this study's experimental conditions and provide preliminary clues about stem-differentiating xylem changes associated with different stresses.

Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants, show strong drought tolerance and environmental adaptability. They are ideal model plants for studying the molecular mechanisms of drought tolerance. Transcriptomic and metabolomic analyses were performed to reveal the response mechanisms of H. ammodendron and H. persicum to a drought environment at the levels of transcription and physiological metabolism. The results showed that the morphological structures of H. ammodendron and H. persicum showed adaptability to drought stress. Under drought conditions, the peroxidase activity, abscisic acid content, auxin content, and gibberellin content of H. ammodendron increased, while the contents of proline and malondialdehyde decreased. The amino acid content of H. persicum was increased, while the contents of proline, malondialdehyde, auxin, and gibberellin were decreased. Under drought conditions, 12,233 and 17,953 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum , respectively, including members of multiple transcription factor families such as FAR1, AP2/ERF, C2H2, bHLH, MYB, C2C2, and WRKY that were significantly up-regulated under drought stress. In the positive ion mode, 296 and 452 differential metabolites (DEMs) were identified in H. ammodendron and H. persicum, respectively; in the negative ion mode, 252 and 354 DEMs were identified, primarily in carbohydrate and lipid metabolism. A combined transcriptome and metabolome analysis showed that drought stress promoted the glycolysis/gluconeogenesis pathways of H. ammodendron and H. persicum and increased the expression of amino acid synthesis pathways, consistent with the physiological results. In addition, transcriptome and metabolome were jointly used to analyze the expression changes of the genes/metabolites of H. ammodendron and H. persicum that were associated with drought tolerance but were regulated differently in the two plants. This study identified drought-tolerance genes and metabolites in H. ammodendron and H. persicum and has provided new ideas for studying the drought stress response of Haloxylon.

Exogenous application of acetic acid enhances drought tolerance by influencing the MAPK signaling pathway induced by ABA and JA in apple plants

The external application of acetic acid (AA) has been shown to improve drought survival in plants, such as Arabidopsis, rice, maize, wheat, rapeseed and cassava, and the application of AA also increased drought tolerance in perennial woody apple (Malus domestica) plants. An understanding of AA-induced drought tolerance in apple plants at the molecular level will contribute to the development of technology that can be used to enhance drought tolerance. In this study, the morphological, physiological and transcriptomic responses to drought stress were analyzed in apple plants after watering without AA (CK), watering with AA (AA), drought treatment (D) and drought treatment with AA (DA). The results suggested that the AA-treated apple plants had a higher tolerance to drought than water-treated plants. Higher levels of chlorophyll and carotenoids were found under the DA conditions than under D stress. The levels of abscisic acid (ABA), jasmonic acid (JA) and methyl jasmonate were increased in AA-treated apple plants. Transcriptomic profiling indicated the key biological pathways involved in metabolic processes, mitogen-activated protein kinase (MAPK) signaling, plant hormone signal transduction and the biosynthesis of secondary metabolites in response to different drought conditions. The 9-cis-epoxycarotenoid dioxygenase, (9S,13S)-cis-oxophytodienoic acid reductase, allene oxide synthase, allene oxide cyclase and lipoxygenase genes participate in the synthase of ABA and JA under drought and AA treatments. Collectively, the results showed that external application of AA enhanced drought tolerance in apple plants by influencing the ABA- and JA-induced MAPK signaling pathways. These data indicated that the application of AA in plants is beneficial for enhancing drought tolerance and decreasing growth inhibition in agricultural fields.

Characterization of the gene expression profile response to drought stress in Haloxylon using PacBio single-molecule real-time and Illumina sequencing

Haloxylon ammodendron and Haloxylon persicum are important drought-tolerant plants in northwest China. The whole-genome sequencing of H. ammodendron and H. persicum grown in their natural environment is incomplete, and their transcriptional regulatory network in response to drought environment remains unclear. To reveal the transcriptional responses of H. ammodendron and H. persicum to an arid environment, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing. In total, 20,246,576 and 908,053 subreads and 435,938 and 210,334 circular consensus sequencing (CCS) reads were identified by SMRT sequencing of H. ammodendron and H. persicum, and 15,238 and 10,135 unigenes, respectively, were successfully obtained. In addition, 9,794 and 7,330 simple sequence repeats (SSRs) and 838 and 71 long non-coding RNAs were identified. In an arid environment, the growth of H. ammodendron was restricted; plant height decreased significantly; basal and branch diameters became thinner and hydrogen peroxide (H₂O₂) content and peroxidase (POD) activity were increased. Under dry and wet conditions, 11,803 and 15,217 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum, respectively. There were 319 and 415 DEGs in the signal transduction pathways related to drought stress signal perception and transmission, including the Ca²⁺ signal pathway, the ABA signal pathway, and the MAPK signal cascade. In addition, 217 transcription factors (TFs) and 398 TFs of H. ammodendron and H. persicum were differentially expressed, including FAR1, MYB, and AP2/ERF. Bioinformatic analysis showed that under drought stress, the expression patterns of genes related to active oxygen [reactive oxygen species (ROS)] scavenging, functional proteins, lignin biosynthesis, and glucose metabolism pathways were altered. Thisis the first full-length transcriptome report concerning the responses of H. ammodendron and H. persicum to drought stress. The results provide a foundation for further study of the adaptation to drought stress. The full-length transcriptome can be used in genetic engineering research.

Physiology and metabonomics reveal differences in drought resistance among soybean varieties

BACKGROUND

The soybean is an important food crop worldwide. Drought during the first pod stage significantly affects soybean yield, and understanding the metabolomic and physiological changes in soybeans under drought stress is crucial. This study identified the differential metabolites in initial pod stage soybean leaves under polyethylene glycol-simulated drought stress, using ultra performance liquid chromatography and tandem mass spectrometry, and the physiological indexes related to drought resistance.

RESULTS

Physiologically, drought resistance also generates enzyme and antioxidant activity; levels of superoxide dismutase, peroxidase, and catalase first increased and subsequently decreased, while those of soluble sugar, soluble protein, malondialdehyde, and proline content increased in both varieties. The contents of CAT, proline and soluble sugar in Heinong 44 (HN44) were higher than those in Heinong 65 (HN65), and the contents of MDA were lower than those in HN65. In metabolomics, the OPLS-DA model was used to screen different metabolites. KEGG analysis showed that the two varieties resisted drought through different ways. Amino acid metabolism and lipid metabolism play a key role in drought resistance of the two varieties, respectively. TCA cycle was one of the core pathways of drought resistance in two varieties. Changes in the content of L-Asparagine and citric acid may be one of the reasons for the difference in drought resistance between the two varieties.

CONCLUSIONS

We think that the reasons of drought resistance among soybean varieties are as follows: the main metabolic pathways are different under drought stress; the contents of metabolites in these metabolic pathways are different; some physiological indexes are different, such as MDA, CAT, proline content and so on. Our study enhances the understanding of the metabolomic soybean drought stress response and provides a reference for soybean drought resistance breeding.

The heat shock factor GhHSFA4a positively regulates cotton resistance to Verticillium dahliae

Heat shock factors (HSFs) play a crucial role in the environmental stress responses of numerous plant species, including defense responses to pathogens; however, their role in cotton resistance to Verticillium dahliae remains unclear. We have previously identified several differentially expressed genes (DEGs) in Arabidopsis thaliana after inoculation with V. dahliae. Here, we discovered that GhHSFA4a in Gossypium hirsutum (cotton) after inoculation with V. dahliae shares a high identity with a DEG in A. thaliana in response to V. dahliae infection. Quantitative real-time PCR (qRT-PCR) analysis indicated that GhHSFA4a expression was rapidly induced by V. dahliae and ubiquitous in cotton roots, stems, and leaves. In a localization analysis using transient expression, GhHSFA4a was shown to be localized to the nucleus. Virus-induced gene silencing (VIGS) revealed that downregulation of GhHSFA4a significantly increased cotton susceptibility to V. dahliae. To investigate GhHSFA4a-mediated defense, 814 DEGs were identified between GhHSFA4a-silenced plants and controls using comparative RNA-seq analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs were enriched in "flavonoid biosynthesis", "sesquiterpenoid and triterpenoid biosynthesis", "linoleic acid metabolism" and "alpha-linolenic acid metabolism". The expression levels of marker genes for these four pathways were triggered after inoculation with V. dahliae. Moreover, GhHSFA4a-overexpressing lines of A. thaliana displayed enhanced resistance against V. dahliae compared to that of the wild type. These results indicate that GhHSFA4a is involved in the synthesis of secondary metabolites and signal transduction, which are indispensable for innate immunity against V. dahliae in cotton.