Molecular insights into plant desiccation tolerance: transcriptomics, proteomics and targeted metabolite profiling in Craterostigma plantagineum

Cell Wall Profiling of the Resurrection Plants Craterostigma plantagineum and Lindernia brevidens and Their Desiccation-Sensitive Relative, Lindernia subracemosa

Vegetative desiccation tolerance has evolved within the genera Craterostigma and Lindernia. A centre of endemism and diversification for these plants appears to occur in ancient tropical montane rainforests of east Africa in Kenya and Tanzania. Lindernia subracemosa, a desiccation-sensitive relative of Craterostigma plantagineum, occurs in these rainforests and experiences adequate rainfall and thus does not require desiccation tolerance. However, sharing this inselberg habitat, another species, Lindernia brevidens, does retain vegetative desiccation tolerance and is also related to the resurrection plant C. plantagineum found in South Africa. Leaf material was collected from all three species at different stages of hydration: fully hydrated (ca. 90% relative water content), half-dry (ca. 45% relative water content) and fully desiccated (ca. 5% relative water content). Cell wall monosaccharide datasets were collected from all three species. Comprehensive microarray polymer profiling (CoMPP) was performed using ca. 27 plant cell-wall-specific antibodies and carbohydrate-binding module probes. Some differences in pectin, xyloglucan and extension epitopes were observed between the selected species. Overall, cell wall compositions were similar, suggesting that wall modifications in response to vegetative desiccation involve subtle cell wall remodelling that is not reflected by the compositional analysis and that the plants and their walls are constitutively protected against desiccation.

Convergent evolution of desiccation tolerance in grasses

Desiccation tolerance has evolved repeatedly in plants as an adaptation to survive extreme environments. Plants use similar biophysical and cellular mechanisms to survive life without water, but convergence at the molecular, gene and regulatory levels remains to be tested. Here we explore the evolutionary mechanisms underlying the recurrent evolution of desiccation tolerance across grasses. We observed substantial convergence in gene duplication and expression patterns associated with desiccation. Syntenic genes of shared origin are activated across species, indicative of parallel evolution. In other cases, similar metabolic pathways are induced but using different gene sets, pointing towards phenotypic convergence. Species-specific mechanisms supplement these shared core mechanisms, underlining the complexity and diversity of evolutionary adaptations to drought. Our findings provide insight into the evolutionary processes driving desiccation tolerance and highlight the roles of parallel and convergent evolution in response to environmental challenges.

Joint transcriptomic and metabolomic analysis provides new insights into drought resistance in watermelon (Citrullus lanatus)

Introduction

Watermelon is an annual vine of the family Cucurbitaceae. Watermelon plants produce a fruit that people love and have important nutritional and economic value. With global warming and deterioration of the ecological environment, abiotic stresses, including drought, have become important factors that impact the yield and quality of watermelon plants. Previous research on watermelon drought resistance has included analyzing homologous genes based on known drought-responsive genes and pathways in other species.

Methods

However, identifying key pathways and genes involved in watermelon drought resistance through high-throughput omics methods is particularly important. In this study, RNA-seq and metabolomic analysis were performed on watermelon plants at five time points (0 h, 1 h, 6 h, 12 h and 24 h) before and after drought stress.

Results

Transcriptomic analysis revealed 7829 differentially expressed genes (DEGs) at the five time points. The DEGs were grouped into five clusters using the k-means clustering algorithm. The functional category for each cluster was annotated based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database; different clusters were associated with different time points after stress. A total of 949 metabolites were divided into 10 categories, with lipids and lipid-like molecules accounting for the most metabolites. Differential expression analysis revealed 22 differentially regulated metabolites (DRMs) among the five time points. Through joint analysis of RNA-seq and metabolome data, the 6-h period was identified as the critical period for watermelon drought resistance, and the starch and sucrose metabolism, plant hormone signal transduction and photosynthesis pathways were identified as important regulatory pathways involved in watermelon drought resistance. In addition, 15 candidate genes associated with watermelon drought resistance were identified through joint RNA-seq and metabolome analysis combined with weighted correlation network analysis (WGCNA). Four of these genes encode transcription factors, including bHLH (Cla97C03G068160), MYB (Cla97C01G002440), HSP (Cla97C02G033390) and GRF (Cla97C02G042620), one key gene in the ABA pathway, SnRK2-4 (Cla97C10G186750), and the GP-2 gene (Cla97C05G105810), which is involved in the starch and sucrose metabolism pathway.

Discussion

In summary, our study provides a theoretical basis for elucidating the molecular mechanisms underlying drought resistance in watermelon plants and provides new genetic resources for the study of drought resistance in this crop.

Comparative differences in maintaining membrane fluidity and remodeling cell wall between Glycine soja and Glycine max leaves under drought

Water shortage is one of the most important environmental factors limiting crop yield. In this study, we used wild soybean (Glycine soja Sieb. et Zucc.) and soybean (Glycinemax (L.) Merr.) seedlings as experimental materials, simulated drought stress using soil gravimetry, measured growth and physiological parameters, and analyzed differentially expressed genes and metabolites in the leaves of seedling by integrated transcriptomics and metabolomics techniques. The results indicate that under water deficit, Glycine soja maintained stable photosynthate by accumulating Mg2+, Fe3+, Mn2+, Zn2+ and B3+, and improved water absorption by increasing root growth. Notably, Glycine soja enhanced linoleic acid metabolism and plasma membrane intrinsic protein (PIP1) gene expression to maintain membrane fluidity, and increased pentose, glucuronate and galactose metabolism and thaumatin protein genes expression to remodel the cell wall, thereby increasing water-absorption to better tolerate to drought stress. In addition, it was found that secondary phenolic metabolism, such as phenylpropane biosynthesis, flavonoid biosynthesis and ascobate and aldarate metabolism were weakened, resulting in the collapse of the antioxidant system, which was the main reason for the sensitivity of Glycine max to drought stress. These results provide new insights into plant adaptation to water deficit and offer a theoretical basis for breeding soybean varieties with drought tolerance.

The impact of dietary Laminaria digitata and alginate lyase supplementation on the weaned piglet liver: A comprehensive proteomics and metabolomics approach

The brown seaweed Laminaria digitata, a novel feedstuff for weaned piglets, has potentially beneficial prebiotic properties. However, its recalcitrant cell wall challenges digestion in monogastrics. Alginate lyase is a promising supplement to mitigate this issue. This study's aim was to investigate the impact of incorporating 10% dietary Laminaria digitata, supplemented with alginate lyase, on the hepatic proteome and metabolome of weaned piglets. These diets introduced minor variations to the metabolome and caused significant shifts in the proteome. Dietary seaweed provided a rich source of n-3 PUFAs that could signal hepatic fatty acid oxidation (FABP, ACADSB and ALDH1B1). This may have affected the oxidative stability of the tissue, requiring an elevated abundance of GST for regulation. The presence of reactive oxygen species likely inflicted protein damage, triggering increased proteolytic activity (LAPTM4B and PSMD4). Alginate lyase supplementation augmented the number of differentially abundant proteins, which included GBE1 and LDHC, contributing to maintain circulating glucose levels by mobilizing glycogen stores and branched-chain amino acids. The enzymatic supplementation with alginate lyase amplified the effects of the seaweed-only diet. An additional filter was employed to test the effect of missing values on the proteomics analysis, which is discussed from a technical perspective. SIGNIFICANCE: Brown seaweeds such as Laminaria digitata have prebiotic and immune-modulatory components, such as laminarin, that can improve weaned piglet health. However, they have recalcitrant cell wall polysaccharides, such as alginate, that can elicit antinutritional effects on the monogastric digestive system. The aim of this study was to evaluate the effect of a high level of dietary L. digitata and alginate lyase supplementation on the hepatic metabolism of weaned piglets, using high throughput Omics approaches.

Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival

The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.

Specific metabolic and cellular mechanisms of the vegetative desiccation tolerance in resurrection plants for adaptation to extreme dryness

MAIN CONCLUSION

Substantial advancements have been made in our comprehension of vegetative desiccation tolerance in resurrection plants, and further research is still warranted to elucidate the mechanisms governing distinct cellular adaptations. Resurrection plants are commonly referred to as a small group of extremophile vascular plants that exhibit vegetative desiccation tolerance (VDT), meaning that their vegetative tissues can survive extreme drought stress (> 90% water loss) and subsequently recover rapidly upon rehydration. In contrast to most vascular plants, which typically employ water-saving strategies to resist partial water loss and optimize water absorption and utilization to a limited extent under moderate drought stress, ultimately succumbing to cell death when confronted with severe and extreme drought conditions, resurrection plants have evolved unique mechanisms of VDT, enabling them to maintain viability even in the absence of water for extended periods, permitting them to rejuvenate without harm upon water contact. Understanding the mechanisms associated with VDT in resurrection plants holds the promise of expanding our understanding of how plants adapt to exceedingly arid environments, a phenomenon increasingly prevalent due to global warming. This review offers an updated and comprehensive overview of recent advances in VDT within resurrection plants, with particular emphasis on elucidating the metabolic and cellular adaptations during desiccation, including the intricate processes of cell wall folding and the prevention of cell death. Furthermore, this review highlights existing unanswered questions in the field, suggests potential avenues for further research to gain deeper insights into the remarkable VDT adaptations observed in resurrection plants, and highlights the potential application of VDT-derived techniques in crop breeding to enhance tolerance to extreme drought stress.

Water content, transition temperature and fragility influence protection and anhydrobiotic capacity

Water is essential for metabolism and all life processes. Despite this, many organisms distributed across the kingdoms of life survive near-complete desiccation or anhydrobiosis. Increased intracellular viscosity, leading to the formation of a vitrified state is necessary, but not sufficient, for survival while dry. What properties of a vitrified system make it desiccation-tolerant or -sensitive are unknown. We have analyzed 18 different in vitro vitrified systems, composed of one of three protective disaccharides (trehalose, sucrose, or maltose) and glycerol, quantifying their enzyme-protective capacity and their material properties in a dry state. Protection conferred by mixtures containing maltose correlates strongly with increased water content, increased glass-transition temperature, and reduced glass former fragility, while the protection of glasses formed with sucrose correlates with increased glass transition temperature and the protection conferred by trehalose glasses correlates with reduced glass former fragility. Thus, in vitro different vitrified sugars confer protection through distinct material properties. Next, we examined the material properties of a dry desiccation tolerant and intolerant life stage from three different organisms. The dried desiccation tolerant life stage of all organisms had an increased glass transition temperature and reduced glass former fragility relative to its dried desiccation intolerant life stage. These results suggest in nature organismal desiccation tolerance relies on a combination of various material properties. This study advances our understanding of how protective and non-protective glasses differ in terms of material properties that promote anhydrobiosis. This knowledge presents avenues to develop novel stabilization technologies for pharmaceuticals that currently rely on the cold-chain.

Statement of significance

For the past three decades the anhydrobiosis field has lived with a paradox, while vitrification is necessary for survival in the dry state, it is not sufficient. Understanding what property(s) distinguishes a desiccation tolerant from an intolerant vitrified system and how anhydrobiotic organisms survive drying is one of the enduring mysteries of organismal physiology. Here we show in vitro the enzyme-protective capacity of different vitrifying sugars can be correlated with distinct material properties. However, in vivo, diverse desiccation tolerant organisms appear to combine these material properties to promote their survival in a dry state.

Transcriptomic and metabolomic profiling reveals the drought tolerance mechanism of Illicium difengpi (Schisandraceae)

Illicium difengpi (Schisandraceae), an endangered medicinal plant endemic to karst areas, is highly tolerant to drought and thus can be used as an ideal material for investigating adaptive mechanism to drought stress. The understanding of the drought tolerance of I. difengpi, especially at the molecular level, is lacking. In the present study, we aimed to clarify the molecular mechanism underlying drought tolerance in endemic I. difengpi plant in karst regions. The response characteristics of transcripts and changes in metabolite abundance of I. difengpi subjected to drought and rehydration were analyzed, the genes and key metabolites responsive to drought and rehydration were screened, and some important biosynthetic and secondary metabolic pathways were identified. A total of 231,784 genes and 632 metabolites were obtained from transcriptome and metabolome analyses, and most of the physiological metabolism in drought-treated I. difengpi plants recovered after rehydration. There were more upregulated genes than downregulated genes under drought and rehydration treatments, and rehydration treatment induced stable expression of 65.25% of genes, indicating that rehydration alleviated drought stress to some extent. Drought and rehydration treatment generated flavonoids, phenolic acids, flavonols, amino acids and their derivatives, as well as metabolites such as saccharides and alcohols in the leaves of I. difengpi plants, which alleviated the injury caused by excessive reactive oxygen species. The integration of transcriptome and metabolome analyses showed that, under drought stress, I. difengpi increased glutathione, flavonoids, polyamines, soluble sugars and amino acids, contributing to cell osmotic potential and antioxidant activity. The results show that the high drought tolerance and recovery after rehydration are the reasons for the normal growth of I. difengpi in karst mountain areas.

The metabolic profiles of Eugenia astringens and E. uniflora (Myrtaceae) sensitive seeds affect desiccation

Myrtaceae species are abundant in tropical Atlantic rainforests, but 41% of the 5500 species of this family are of extreme conservation concern. Eugenia astringens and E. uniflora are native Brazilian Myrtaceae species that occur in the same habitats and produce desiccation-sensitive (DS) seeds. We hypothesized that their seed desiccation-sensitivity degree is associated with specific metabolic signatures. To test it, we analyzed the germination and metabolic profiles of fresh and desiccated seeds. The water content (WC) at which at least half of the seeds survived desiccation was lower in E. astringens (0.17 g H2 O g-1 DW) than in E. uniflora (0.41 g H2 O g-1 DW). We identified 103 annotated metabolites from 3261 peaks in both species, which differed in their relative contents between E. astringens and E. uniflora seeds. The main differences in seed metabolic profiles include several protective molecules in the group of carbohydrates and organic acids and amino acid contents. The relative contents of monosaccharides and disaccharides, malic and quinic acids, amino acids and saturated fatty acids may have taken part in the distinct DS behaviour of E. astringens and E. uniflora seeds. Our study provides evidence of the relationship between desiccation sensitivity, seed viability and metabolic profile of tropical seeds by comparing two closely related Eugenia species with different DS degrees.

Integrated transcriptome and metabolome revealed the drought responsive metabolic pathways in Oriental Lily (Lilium L.)

Objective

Lily is an essential ornamental flowering species worldwide. Drought stress is a major constraint affecting the morphology and physiology and lily leaves and flowers. Therefore, understanding the molecular mechanism underlying lily response to drought stress is important.

Method

Transcriptome and metabolome analysis were performed on Oriental Lily subjected to drought stress.

Result

Most transcription factors and metabolites yielded by the conjoint analysis displayed a downregulated expression pattern. Differential genes and metabolites mainly co-enriched in glycolic pathways related to sugars, such as galactose, and sucrose, glycolysis and gluconeogenesis, indicating that drought stress reduced the sugar metabolism level of Oriental Lily. Combined with transcriptome and metabolome data, nine pairs of differentially expressed metabolites and the genes (p < 0.05) were obtained. Interestingly, a gene named TRINITY_DN2608 (encoding a type of alpha-D-glucose) cloned and its overexpression lines in Arabidopsis thaliana was generated. Overexpression of TRINITY_DN2608 gene elevated the susceptibility to drought stress possibly by suppressing the glucose level.

Conclusion

The enrichment of sugar-related pathways advocates the potential role of glucose metabolism in drought stress. Our study provides theoretical information related to the glucose-mediated drought response and would be fruitful in future lily breeding programs.

Metabolomic Analysis of the Desert Moss Syntrichia caninervis Provides Insights into Plant Dehydration and Rehydration Response

Desiccation-tolerant (DT) plants can survive extreme dehydration and tolerate the loss of up to 95% of their water content, making them ideal systems to determine the mechanism behind extreme drought stress and identify potential approaches for developing drought-tolerant crops. The desert moss Syntrichia caninervis is an emerging model for extreme desiccation tolerance that has benefited from high-throughput sequencing analyses, allowing identification of stress-tolerant genes; however, its metabolic response to desiccation is unknown. A liquid chromatography-mass spectrometry analysis of S. caninervis at six dehydration-rehydration stages revealed 912 differentially abundant compounds, belonging to 93 metabolic classes. Many (256) metabolites accumulated during rehydration in S. caninervis, whereas only 71 accumulated during the dehydration period, in contrast to the pattern observed in vascular DT plants. During dehydration, nitrogenous amino acids (l-glutamic acid and cysteinylglycine), alkaloids (vinleurosine) and steroids (physalin D) accumulated, whereas glucose 6-phosphate decreased. During rehydration, γ-aminobutyric acid, glucose 6-phosphate and flavonoids (karanjin and aromadendrin) accumulated, as did the plant hormones 12-oxo phytodienoic acid (12-OPDA) and trans-zeatin riboside. The contents ofl-arginine, maltose, turanose, lactulose and sucrose remained high throughout dehydration-rehydration. Syntrichia caninervis thus accumulates antioxidants to scavenge reactive oxygen species, accumulating nitrogenous amino acids and cytoprotective metabolites and decreasing energy metabolism to enter a protective state from dehydration-induced damage. During subsequent rehydration, many metabolites rapidly accumulated to prevent oxidative stress and restore physiological activities while repairing cells, representing a more elaborate rehydration repair mechanism than vascular DT plants, with a faster and greater accumulation of metabolites. This metabolic kinetics analysis in S. caninervis deepens our understanding of its dehydration mechanisms and provides new insights into the different strategies of plant responses to dehydration and rehydration.

A horizontal view of primary metabolomes in vegetative desiccation tolerance

Vegetative desiccation tolerance (VDT), the ability of such tissues to survive the near complete loss of cellular water, is a rare but polyphyletic phenotype. It is a complex multifactorial trait, typified by universal (core) factors but with many and varied adaptations due to plant architecture, biochemistry and biotic/abiotic dynamics of particular ecological niches. The ability to enter into a quiescent biophysically stable state is what ultimately determines desiccation tolerance. Thus, understanding the metabolomic complement of plants with VDT gives insight into the nature of survival as well as evolutionary aspects of VDT. In this study, we measured the soluble carbohydrate profiles and the polar, TMS-derivatisable metabolomes of 7 phylogenetically diverse species with VDT, in contrast with two desiccation sensitive (DS) species, under conditions of full hydration, severe water deficit stress, and desiccation. Our study confirmed the existence of core mechanisms of VDT systems associated with either constitutively abundant trehalose or the accumulation of raffinose family oligosaccharides and sucrose, with threshold ratios conditioned by other features of the metabolome. DS systems did not meet these ratios. Considerable chemical variations among VDT species suggest that co-occurring but distinct stresses (e.g., photooxidative stress) are dealt with using different chemical regimes. Furthermore, differences in the timing of metabolic shifts suggest there is not a single "desiccation programme" but that subprocesses are coordinated differently at different drying phases. There are likely to be constraints on the composition of a viable dry state and how different adaptive strategies interact with the biophysical constraints of VDT.

Enhanced ileum function in weaned piglets via Laminaria digitata and alginate lyase dietary inclusion: A combined proteomics and metabolomics analysis

Laminaria digitata, a brown seaweed with prebiotic properties, can potentially enhance the resilience of weaned piglets to nutritional distress. However, their cell wall polysaccharides elude digestion by monogastric animals' endogenous enzymes. In vitro studies suggest alginate lyase's ability to degrade such polysaccharides. This study aimed to assess the impact of a 10% dietary inclusion of L. digitata and alginate lyase supplementation on the ileum proteome and metabolome, adopting a hypothesis-generating approach. Findings indicated that control piglets escalated glucose usage as an enteric energy source, as evidenced by the increased abundance of PKLR and PCK2 proteins and decreased tissue glucose concentration. Additionally, the inclusion of seaweed fostered a rise in proteins linked to enhanced enterocyte structural integrity (ACTBL2, CRMP1, FLII, EML2 and MYLK), elevated peptidase activity (NAALADL1 and CAPNS1), and heightened anti-inflammatory activity (C3), underscoring improved intestinal function. In addition, seaweed-fed piglets showed a reduced abundance of proteins related to apoptosis (ERN2) and proteolysis (DPP4). Alginate lyase supplementation appeared to amplify the initial effects of seaweed-only feeding, by boosting the number of differential proteins within the same pathways. This amplification is potentially due to increased intracellular nutrient availability, making a compelling case for further exploration of this dietary approach. SIGNIFICANCE: Pig production used to rely heavily on antibiotics and zinc oxide to deal with post-weaning stress in a cost-effective way. Their negative repercussions on public health and the environment have motivated heavy restrictions, and a consequent search for alternative feed ingredients/supplements. One of such alternatives is Laminaria digitata, a brown seaweed whose prebiotic components that can help weaned piglets deal with nutritional stress, by improving their gut health and immune status. However, their recalcitrant cell walls have antinutritional properties, for which alginate lyase supplementation is a possible solution. By evaluating ileal metabolism as influenced by dietary seaweed and enzyme supplementation, we aim at discovering how the weaned piglet adapts to them and what are their effects on this important segment of the digestive system.

A review of the role of metabolites in vegetative desiccation tolerance of angiosperms

The survival of extreme water deficit stress by tolerant organisms requires a coordinated series of responses, including those at cellular, transcriptional, translational and metabolic levels. Small molecules play a pivotal role in creating the proper chemical environment for the preservation of cellular integrity and homeostasis during dehydration. This review surveys recent insights in the importance of primary and specialised metabolites in the response to drying of angiosperms with vegetative desiccation tolerance, i.e. the ability to survive near total loss of water. Important metabolites include sugars such as sucrose, trehalose and raffinose family of oligosaccharides, amino acids and organic acids, as well as antioxidants, representing a common core mechanism of desiccation tolerance. Additional metabolites are discussed in the context of species specificity and adaptation.

Multiomics reveals Claroideoglomus etunicatum regulates plant hormone signal transduction, photosynthesis and La compartmentalization in maize to promote growth under La stress

Rare earth elements (REEs) have been widely used in traditional and high-tech fields, and high doses of REEs are considered a risk to the ecosystem. Although the influence of arbuscular mycorrhizal fungi (AMF) in promoting host resistance to heavy metal (HM) stress has been well documented, the molecular mechanism by which AMF symbiosis enhances plant tolerance to REEs is still unclear. A pot experiment was conducted to investigate the molecular mechanism by which the AMF Claroideoglomus etunicatum promotes maize (Zea mays) seedling tolerance to lanthanum (La) stress (100 mg·kg^-1 La). C. etunicatum symbiosis significantly improved maize seedling growth, P and La uptake and photosynthesis. Transcriptome, proteome, and metabolome analyses performed alone and together revealed that differentially expressed genes (DEGs) related to auxin /indole-3-acetic acid (AUX/IAA) and the DEGs and differentially expressed proteins (DEPs) related to ATP-binding cassette (ABC) transporters, natural resistance-associated macrophage proteins (Nramp6), vacuoles and vesicles were upregulated. In contrast, photosynthesis-related DEGs and DEPs were downregulated, and 1-phosphatidyl-1D-myo-inositol 3-phosphate (PI(3)P) was more abundant under C. etunicatum symbiosis. C. etunicatum symbiosis can promote plant growth by increasing P uptake, regulating plant hormone signal transduction, photosynthesis and glycerophospholipid metabolism pathways and enhancing La transport and compartmentalization in vacuoles and vesicles. The results provide new insights into the promotion of plant REE tolerance by AMF symbiosis and the possibility of utilizing AMF-maize interactions in REE phytoremediation and recycling.

Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton

Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.

Transcriptome and proteome depth analysis indicate ABA, MAPK cascade and Ca2+ signaling co-regulate cold tolerance in Rhododendron chrysanthum Pall

INTRODUCTION

Cold stress is a global common problem that significantly limits plant development and geographical distribution. Plants respond to low temperature stress by evolving interrelated regulatory pathways to respond and adapt to their environment in a timely manner. Rhodoendron chrysanthum Pall. (R. chrysanthum) is a perennial evergreen dwarf shrub used for adornment and medicine that thrives in the Changbai Mountains at high elevations and subfreezing conditions.

METHODS

In this study, a comprehensive investigation of cold tolerance (4°C, 12h) in R. chrysanthum leaves under cold using physiological combined with transcriptomic and proteomic approaches.

RESULTS

There were 12,261 differentially expressed genes (DEGs) and 360 differentially expressed proteins (DEPs) in the low temperature (LT) and normal treatment (Control). Integrated transcriptomic and proteomic analyses showed that MAPK cascade, ABA biosynthesis and signaling, plant-pathogen interaction, linoleic acid metabolism and glycerophospholipid metabolism were significantly enriched in response to cold stress of R. chrysanthum leaves.

DISCUSSION

We analyzed the involvement of ABA biosynthesis and signaling, MAPK cascade, and Ca²⁺ signaling, that may jointly respond to stomatal closure, chlorophyll degradation, and ROS homeostasis under low temperature stress. These results propose an integrated regulatory network of ABA, MAPK cascade and Ca²⁺ signaling comodulating the cold stress in R. chrysanthum, which will provide some insights to elucidate the molecular mechanisms of cold tolerance in plants.

Proteomic and Transcriptomic Responses of the Desiccation-Tolerant Moss Racomitrium canescens in the Rapid Rehydration Processes

The moss Racomitrium canescens (R. canescens) has strong desiccation tolerance. It can remain desiccated for years and yet recover within minutes of rehydration. Understanding the responses and mechanisms underlying this rapid rehydration capacity in bryophytes could identify candidate genes that improve crop drought tolerance. We explored these responses using physiology, proteomics, and transcriptomics. Label-free quantitative proteomics comparing desiccated plants and samples rehydrated for 1 min or 6 h suggesting that damage to chromatin and the cytoskeleton had occurred during desiccation, and pointing to the large-scale degradation of proteins, the production of mannose and xylose, and the degradation of trehalose immediately after rehydration. The assembly and quantification of transcriptomes from R. canescens across different stages of rehydration established that desiccation was physiologically stressful for the plants; however, the plants recovered rapidly once rehydrated. According to the transcriptomics data, vacuoles appear to play a crucial role in the early stages of R. canescens recovery. Mitochondria and cell reproduction might recover before photosynthesis; most biological functions potentially restarted after ~6 h. Furthermore, we identified novel genes and proteins related to desiccation tolerance in bryophytes. Overall, this study provides new strategies for analyzing desiccation-tolerant bryophytes and identifying candidate genes for improving plant drought tolerance.

Protein Changes in Shade and Sun Haberlea rhodopensis Leaves during Dehydration at Optimal and Low Temperatures

Haberlea rhodopensis is a unique resurrection plant of high phenotypic plasticity, colonizing both shady habitats and sun-exposed rock clefts. H. rhodopensis also survives freezing winter temperatures in temperate climates. Although survival in conditions of desiccation and survival in conditions of frost share high morphological and physiological similarities, proteomic changes lying behind these mechanisms are hardly studied. Thus, we aimed to reveal ecotype-level and temperature-dependent variations in the protective mechanisms by applying both targeted and untargeted proteomic approaches. Drought-induced desiccation enhanced superoxide dismutase (SOD) activity, but FeSOD and Cu/ZnSOD-III were significantly better triggered in sun plants. Desiccation resulted in the accumulation of enzymes involved in carbohydrate/phenylpropanoid metabolism (enolase, triosephosphate isomerase, UDP-D-apiose/UDP-D-xylose synthase 2, 81E8-like cytochrome P450 monooxygenase) and protective proteins such as vicinal oxygen chelate metalloenzyme superfamily and early light-induced proteins, dehydrins, and small heat shock proteins, the latter two typically being found in the latest phases of dehydration and being more pronounced in sun plants. Although low temperature and drought stress-induced desiccation trigger similar responses, the natural variation of these responses in shade and sun plants calls for attention to the pre-conditioning/priming effects that have high importance both in the desiccation responses and successful stress recovery.

A molecular study of Italian ryegrass grown on Martian regolith simulant

In the last decade, the exploration of deep space has become the objective of the national space programs of many countries. The International Space Exploration Coordination Group has set a roadmap whose long-range strategy envisions the expansion of human presence in the solar system to progress with exploration and knowledge and to accelerate innovation. Crewed missions to Mars could be envisaged by 2040. In this scenario, finding ways to use the local resources for the provision of food, construction materials, propellants, pharmaceuticals is needed. Plants are important resources for deep space manned missions because they produce phytochemicals of pharmaceutical relevance, are sources of food and provide oxygen which is crucial in bioregenerative life support systems. Growth analysis and plant biomass yield have been previously evaluated on Martian regolith simulants; however, molecular approaches employing gene expression analysis and proteomics are still missing. The present work aims at filling this gap by providing molecular data on a representative member of the Poaceae, Lolium multiflorum Lam., grown on potting soil and a Martian regolith simulant (MMS-1). The molecular data were complemented with optical microscopy of root/leaf tissues and physico-chemical analyses. The results show that the plants grew for 2 weeks on regolith simulants. The leaves were bent downwards and chlorotic, the roots developed a lacunar aerenchyma and small brownish deposits containing Fe were observed. Gene expression analysis and proteomics revealed changes in transcripts related to the phenylpropanoid pathway, stress response, primary metabolism and proteins involved in translation and DNA methylation. Additionally, the growth of plants slightly but significantly modified the pH of the regolith simulants. The results here presented constitute a useful resource to get a comprehensive understanding of the major factors impacting the growth of plants on MMS-1.

Integrated analyses reveal the response of peanut to phosphorus deficiency on phenotype, transcriptome and metabolome

BACKGROUND

Phosphorus (P) is one of the most essential macronutrients for crops. The growth and yield of peanut (Arachis hypogaea L.) are always limited by P deficiency. However, the transcriptional and metabolic regulatory mechanisms were less studied. In this study, valuable phenotype, transcriptome and metabolome data were analyzed to illustrate the regulatory mechanisms of peanut under P deficiency stress.

RESULT

In present study, two treatments of P level in deficiency with no P application (-P) and in sufficiency with 0.6 mM P application (+ P) were used to investigate the response of peanut on morphology, physiology, transcriptome, microRNAs (miRNAs), and metabolome characterizations. The growth and development of plants were significantly inhibited under -P treatment. A total of 6088 differentially expressed genes (DEGs) were identified including several transcription factor family genes, phosphate transporter genes, hormone metabolism related genes and antioxidant enzyme related genes that highly related to P deficiency stress. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that 117 genes were annotated in the phenylpropanoid biosynthesis pathway under P deficiency stress. A total of 6 miRNAs have been identified significantly differential expression between + P and -P group by high-throughput sequencing of miRNAs, including two up-regulated miRNAs (ahy-miR160-5p and ahy-miR3518) and four down-regulated miRNAs (ahy-miR408-5p, ahy-miR408-3p, ahy-miR398, and ahy-miR3515). Further, the predicted 22 target genes for 6 miRNAs and cis-elements in 2000 bp promoter region of miRNA genes were analyzed. A total of 439 differentially accumulated metabolites (DAMs) showed obviously differences in two experimental conditions.

CONCLUSIONS

According to the result of transcripome and metabolome analyses, we can draw a conclusion that by increasing the content of lignin, amino acids, and levan combining with decreasing the content of LPC, cell reduced permeability, maintained stability, raised the antioxidant capacity, and increased the P uptake in struggling for survival under P deficiency stress.

Mitochondrial activity and biogenesis during resurrection of Haberlea rhodopensis

Haberlea rhodopensis is a resurrection plant that can tolerate extreme and prolonged periods of desiccation with a rapid restoration of physiological function upon rehydration. Specialized mechanisms are required to minimize cellular damage during desiccation and to maintain integrity for rapid recovery following rehydration. In this study we used respiratory activity measurements, electron microscopy, transcript, protein and blue native-PAGE analysis to investigate mitochondrial activity and biogenesis in fresh, desiccated and rehydrated detached H. rhodopensis leaves. We demonstrate that unlike photosynthesis, mitochondrial respiration was almost immediately activated to levels of fresh tissue upon rehydration. The abundance of transcripts and proteins involved in mitochondrial respiration and biogenesis were at comparable levels in fresh, desiccated and rehydrated tissues. Blue native-PAGE analysis revealed fully assembled and equally abundant OXPHOS complexes in mitochondria isolated from fresh, desiccated and rehydrated detached leaves. We observed a high abundance of alternative respiratory components which correlates with the observed high uncoupled respiration capacity in desiccated tissue. Our study reveals that during desiccation of vascular H. rhodopensis tissue, mitochondrial composition is conserved and maintained at a functional state allowing for an almost immediate activation to full capacity upon rehydration. Mitochondria-specific mechanisms were activated during desiccation which probably play a role in maintaining tolerance.

Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis

Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.

Studies on the molecular level changes and potential resistance mechanism of Coreius guichenoti under temperature stimulation

In this study, we used transcriptome and proteome technology to analyze molecular level changes in tissues of Coreius guichenoti cultured at high temperature (HT) and low temperature (LT). We also screened for specific anti-stress genes and proteins and evaluated the relationships between them. We identified 201,803 unigenes and 10,623 proteins. Compared with the normal temperature (NT), 408 genes and 1,204 proteins were up- or down-regulated in brain tissues, respectively, at HT, and the numbers were 8 and 149 at LT. In gill tissues, the numbers were 101 and 1,745 at HT and 27 and 511 at LT. In gill tissues at both temperatures, the degree of down-regulation (average, HT 204.67-fold, LT 443.13-fold) was much greater than that of up-regulation (average, HT 28.69-fold, LT 17.68-fold). The protein expression in brain (average, up 52.67-fold, down 13.54-fold) and gill (average, up 73.02-fold, down 12.92-fold) tissues increased more at HT than at LT. The protein expression in brain (up 3.77-fold, down 4.79-fold) tissues decreased more at LT than at HT, whereas the protein expression in gill (up 8.64-fold, down 4.35-fold) tissues was up-regulated more at LT than at HT. At HT, brain tissues were mainly enriched in pathways related to metabolism and DNA repair; at LT, they were mainly enriched in cancer-related pathways. At both temperatures, gill tissues were mainly enriched in pathways related to cell proliferation, apoptosis, immunity, and inflammation. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed more differentially expressed proteins in gill tissues than in brain tissues at HT and LT, and temperature stimulation led to the strengthening of metabolic pathways in both tissues. Of the 96 genes we identified as potentially being highly related to temperature stress (59 from transcriptome and 38 from proteome data), we detected heat shock protein 70 in both the transcriptome and proteome. Our results improved our understanding of the differential relationship between gene expression and protein expression in C. guichenoti. Identifying important temperature stress genes will help lay a foundation for cultivating C. guichenoti, and even other fish species, that are resistant to HT or LT.

Water retention and metabolic changes improve desiccation tolerance in Barbacenia graminifolia (Velloziaceae)

Barbacenia graminifolia is a Velloziaceae species endemic to the campos rupestres in Serra do Cipó, Minas Gerais state (Brazil). This biome is characterised by high irradiance and limited water conditions. Unlike other resurrection plants, B. graminifolia can maintain a high hydric status (>80%) after 28 days of water suppression before desiccation. We investigated the physiological and metabolic mechanisms associated with structural changes that allow B. graminifolia to maintain hydration under a prolonged water deficit and to recover after desiccation. After 30 days of water deficit, desiccated plants exhibited chlorophyll degradation, a 178.4% and 193.7% increase in total carotenoids and MDA, respectively, and twice the CAT and APX activity compared to hydrated plants. The metabolite profile showed increased amino acids, carbohydrates, saturated fatty acids and benzoic acids during dehydration, while trichloroacetic acid cycle acids were higher in hydrated and rehydrated plants. Anatomical and ultrastructural data corroborated the physiological and metabolic changes and revealed the presence of mucilaginous cells with high water retention capacity. Our data indicated that combined strategies of assimilatory metabolism shutdown, accumulation of compatible solutes and antioxidant compounds, increase in hydrophilic molecules, changes in the composition of membrane lipids and remodelling of cell organelles conditioned the efficiency of B. graminifolia in delaying water loss, tolerating further desiccation and quickly recovering after rehydration. These attributes evidence that this species is well adapted to cope with adverse environmental conditions, mainly directing the metabolism to an efficient antioxidant response and improving its capacity to retain water during the dry season.

Proteomics Evidence of a Systemic Response to Desiccation in the Resurrection Plant Haberlea rhodopensis

Global warming and drought stress are expected to have a negative impact on agricultural productivity. Desiccation-tolerant species, which are able to tolerate the almost complete desiccation of their vegetative tissues, are appropriate models to study extreme drought tolerance and identify novel approaches to improve the resistance of crops to drought stress. In the present study, to better understand what makes resurrection plants extremely tolerant to drought, we performed transmission electron microscopy and integrative large-scale proteomics, including organellar and phosphorylation proteomics, and combined these investigations with previously published transcriptomic and metabolomics data from the resurrection plant Haberlea rhodopensis. The results revealed new evidence about organelle and cell preservation, posttranscriptional and posttranslational regulation, photosynthesis, primary metabolism, autophagy, and cell death in response to desiccation in H. rhodopensis. Different protective intrinsically disordered proteins, such as late embryogenesis abundant (LEA) proteins, thaumatin-like proteins (TLPs), and heat shock proteins (HSPs), were detected. We also found a constitutively abundant dehydrin in H. rhodopensis whose phosphorylation levels increased under stress in the chloroplast fraction. This integrative multi-omics analysis revealed a systemic response to desiccation in H. rhodopensis and certain targets for further genomic and evolutionary studies on DT mechanisms and genetic engineering towards the improvement of drought tolerance in crops.

Exploring the High Variability of Vegetative Desiccation Tolerance in Pteridophytes

In the context of plant evolution, pteridophytes, which is comprised of lycophytes and ferns, occupy an intermediate position between bryophytes and seed plants, sharing characteristics with both groups. Pteridophytes is a highly diverse group of plant species that occupy a wide range of habitats including ecosystems with extreme climatic conditions. There is a significant number of pteridophytes that can tolerate desiccation by temporarily arresting their metabolism in the dry state and reactivating it upon rehydration. Desiccation-tolerant pteridophytes exhibit a strategy that appears to be intermediate between the constitutive and inducible desiccation tolerance (DT) mechanisms observed in bryophytes and angiosperms, respectively. In this review, we first describe the incidence and anatomical diversity of desiccation-tolerant pteridophytes and discuss recent advances on the origin of DT in vascular plants. Then, we summarize the highly diverse adaptations and mechanisms exhibited by this group and describe how some of these plants could exhibit tolerance to multiple types of abiotic stress. Research on the evolution and regulation of DT in different lineages is crucial to understand how plants have adapted to extreme environments. Thus, in the current scenario of climate change, the knowledge of the whole landscape of DT strategies is of vital importance as a potential basis to improve plant abiotic stress tolerance.

Desiccation Tolerance in Ramonda serbica Panc.: An Integrative Transcriptomic, Proteomic, Metabolite and Photosynthetic Study

The resurrection plant Ramonda serbica Panc. survives long desiccation periods and fully recovers metabolic functions within one day upon watering. This study aimed to identify key candidates and pathways involved in desiccation tolerance in R. serbica. We combined differential transcriptomics and proteomics, phenolic and sugar analysis, FTIR analysis of the cell wall polymers, and detailed analysis of the photosynthetic electron transport (PET) chain. The proteomic analysis allowed the relative quantification of 1192 different protein groups, of which 408 were differentially abundant between hydrated (HL) and desiccated leaves (DL). Almost all differentially abundant proteins related to photosynthetic processes were less abundant, while chlorophyll fluorescence measurements implied shifting from linear PET to cyclic electron transport (CET). The levels of H2O2 scavenging enzymes, ascorbate-glutathione cycle components, catalases, peroxiredoxins, Fe-, and Mn superoxide dismutase (SOD) were reduced in DL. However, six germin-like proteins (GLPs), four Cu/ZnSOD isoforms, three polyphenol oxidases, and 22 late embryogenesis abundant proteins (LEAPs; mainly LEA4 and dehydrins), were desiccation-inducible. Desiccation provoked cell wall remodeling related to GLP-derived H2O2/HO● activity and pectin demethylesterification. This comprehensive study contributes to understanding the role and regulation of the main metabolic pathways during desiccation aiming at crop drought tolerance improvement.

Two Decades of Desiccation Biology: A Systematic Review of the Best Studied Angiosperm Resurrection Plants

Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models to understand the complex biology of vegetative desiccation tolerance. Despite extensive studies of resurrection plants, many details underlying the mechanisms of desiccation tolerance remain unexplored. To summarize the progress in resurrection plant research and identify unexplored questions, we conducted a systematic review of 15 model angiosperm resurrection plants. This systematic review provides an overview of publication trends on resurrection plants, the geographical distribution of species and studies, and the methodology used. Using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol we surveyed all publications on resurrection plants from 2000 and 2020. This yielded 185 empirical articles that matched our selection criteria. The most investigated plants were Craterostigma plantagineum (17.5%), Haberlea rhodopensis (13.7%), Xerophyta viscosa (reclassified as X. schlechteri) (11.9%), Myrothamnus flabellifolia (8.5%), and Boea hygrometrica (8.1%), with all other species accounting for less than 8% of publications. The majority of studies have been conducted in South Africa, Bulgaria, Germany, and China, but there are contributions from across the globe. Most studies were led by researchers working within the native range of the focal species, but some international and collaborative studies were also identified. The number of annual publications fluctuated, with a large but temporary increase in 2008. Many studies have employed physiological and transcriptomic methodologies to investigate the leaves of resurrection plants, but there was a paucity of studies on roots and only one metagenomic study was recovered. Based on these findings we suggest that future research focuses on resurrection plant roots and microbiome interactions to explore microbial communities associated with these plants, and their role in vegetative desiccation tolerance.

Crops for dry environments

Climate change necessitates increased stress resilience of food crops. We describe four potential solutions, with emphasis on a relatively novel approach aiming at true tolerance of drought rather than improved water-holding capacity of crops, which is a common approach in current breeding and genome editing efforts. Some Angiosperms are known to tolerate loss of 95% of their cellular water, without dying, not dissimilar to seeds. The molecular mechanisms and their regulation underlying this remarkable ability are potentially useful to design tolerant crops. Since most crops produce desiccation tolerant seeds, genomic information for this attribute is present but inactive in vegetative parts of the plant. Based on recent evidence from both seeds and desiccation tolerant Angiosperms we address possible routes to 'flipping the switch' to vegetative desiccation tolerance in major crops.

A Label-Free Proteomic and Complementary Metabolomic Analysis of Leaves of the Resurrection Plant Xerophytaschlechteri during Dehydration

Vegetative desiccation tolerance, or the ability to survive the loss of ~95% relative water content (RWC), is rare in angiosperms, with these being commonly called resurrection plants. It is a complex multigenic and multi-factorial trait, with its understanding requiring a comprehensive systems biology approach. The aim of the current study was to conduct a label-free proteomic analysis of leaves of the resurrection plant Xerophyta schlechteri in response to desiccation. A targeted metabolomics approach was validated and correlated to the proteomics, contributing the missing link in studies on this species. Three physiological stages were identified: an early response to drying, during which the leaf tissues declined from full turgor to a RWC of ~80–70%, a mid-response in which the RWC declined to 40% and a late response where the tissues declined to 10% RWC. We identified 517 distinct proteins that were differentially expressed, of which 253 proteins were upregulated and 264 were downregulated in response to the three drying stages. Metabolomics analyses, which included monitoring the levels of a selection of phytohormones, amino acids, sugars, sugar alcohols, fatty acids and organic acids in response to dehydration, correlated with some of the proteomic differences, giving insight into the biological processes apparently involved in desiccation tolerance in this species.

Systems biology of resurrection plants

Plant species that exhibit vegetative desiccation tolerance can survive extreme desiccation for months and resume normal physiological activities upon re-watering. Here we survey the recent knowledge gathered from the sequenced genomes of angiosperm and non-angiosperm desiccation-tolerant plants (resurrection plants) and highlight some distinct genes and gene families that are central to the desiccation response. Furthermore, we review the vast amount of data accumulated from analyses of transcriptomes and metabolomes of resurrection species exposed to desiccation and subsequent rehydration, which allows us to build a systems biology view on the molecular and genetic mechanisms of desiccation tolerance in plants.

The Cell Wall Proteome of Craterostigma plantagineum Cell Cultures Habituated to Dichlobenil and Isoxaben

The remarkable desiccation tolerance of the vegetative tissues in the resurrection species Craterostigma plantagineum (Hochst.) is favored by its unique cell wall folding mechanism that allows the ordered and reversible shrinking of the cells without damaging neither the cell wall nor the underlying plasma membrane. The ability to withstand extreme drought is also maintained in abscisic acid pre-treated calli, which can be cultured both on solid and in liquid culture media. Cell wall research has greatly advanced, thanks to the use of inhibitors affecting the biosynthesis of e.g., cellulose, since they allowed the identification of the compensatory mechanisms underlying habituation. Considering the innate cell wall plasticity of C. plantagineum, the goal of this investigation was to understand whether habituation to the cellulose biosynthesis inhibitors dichlobenil and isoxaben entailed or not identical mechanisms as known for non-resurrection species and to decipher the cell wall proteome of habituated cells. The results showed that exposure of C. plantagineum calli/cells triggered abnormal phenotypes, as reported in non-resurrection species. Additionally, the data demonstrated that it was possible to habituate Craterostigma cells to dichlobenil and isoxaben and that gene expression and protein abundance did not follow the same trend. Shotgun and gel-based proteomics revealed a common set of proteins induced upon habituation, but also identified candidates solely induced by habituation to one of the two inhibitors. Finally, it is hypothesized that alterations in auxin levels are responsible for the increased abundance of cell wall-related proteins upon habituation.