Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum

Desiccation tolerance in the resurrection plant Barbacenia graminifolia involves changes in redox metabolism and carotenoid oxidation

Desiccation tolerance in vegetative tissues enables resurrection plants to remain quiescent under severe drought and rapidly recover full metabolism once water becomes available. Barbacenia graminifolia is a resurrection plant that occurs at high altitudes, typically growing on rock slits, exposed to high irradiance and limited water availability. We analyzed the levels of reactive oxygen species (ROS) and antioxidants, carotenoids and its cleavage products, and stress-related phytohormones in fully hydrated, dehydrated, and rehydrated leaves of B. graminifolia. This species exhibited a precise adjustment of its antioxidant metabolism to desiccation. Our results indicate that this adjustment is associated with enhanced carotenoid and apocarotenoids, α-tocopherol and compounds of ascorbate-glutathione cycle. While α-carotene and lutein increased in dried-leaves suggesting effective protection of the light-harvesting complexes, the decrease in β-carotene was accompanied of 10.2-fold increase in the content of β-cyclocitral, an apocarotenoid implicated in the regulation of abiotic stresses, compared to hydrated plants. The principal component analysis showed that dehydrated plants at 30 days formed a separate cluster from both hydrated and dehydrated plants for up to 15 days. This regulation might be part of the protective metabolic strategies employed by this resurrection plant to survive water scarcity in its inhospitable habitat.

Core cellular and tissue-specific mechanisms enable desiccation tolerance in Craterostigma

Resurrection plants can survive prolonged life without water (anhydrobiosis) in regions with seasonal drying. This desiccation tolerance requires the coordination of numerous cellular processes across space and time, and individual plant tissues face unique constraints related to their function. Here, we analyzed the complex, octoploid genome of the model resurrection plant Craterostigma (C. plantagineum), and surveyed spatial and temporal expression dynamics to identify genetic elements underlying desiccation tolerance. Homeologous genes within the Craterostigma genome have divergent expression profiles, suggesting the subgenomes contribute differently to desiccation tolerance traits. The Craterostigma genome contains almost 200 tandemly duplicated early light-induced proteins, a hallmark trait of desiccation tolerance, with massive upregulation under water deficit. We identified a core network of desiccation-responsive genes across all tissues, but observed almost entirely unique expression dynamics in each tissue during recovery. Roots and leaves have differential responses related to light and photoprotection, autophagy and nutrient transport, reflecting their divergent functions. Our findings highlight a universal set of likely ancestral desiccation tolerance mechanisms to protect cellular macromolecules under anhydrobiosis, with secondary adaptations related to tissue function.

Ecophysiological Differentiation among Two Resurrection Ferns and Their Allopolyploid Derivative

Theoretically, the coexistence of diploids and related polyploids is constrained by reproductive and competitive mechanisms. Although niche differentiation can explain the commonly observed co-occurrence of cytotypes, the underlying ecophysiological differentiation among cytotypes has hardly been studied. We compared the leaf functional traits of the allotetraploid resurrection fern Oeosporangium tinaei (HHPP) and its diploid parents, O. hispanicum (HH) and O. pteridioides (PP), coexisting in the same location. Our experimental results showed that all three species can recover physiological status after severe leaf dehydration, which confirms their 'resurrection' ability. However, compared with PP, HH had much higher investment per unit area of light-capturing surface, lower carbon assimilation rate per unit mass for the same midday water potential, higher non-enzymatic antioxidant capacity, higher carbon content, and lower contents of nitrogen, phosphorus, and other macronutrients. These traits allow HH to live in microhabitats with less availability of water and nutrients (rock crevices) and to have a greater capacity for resurrection. The higher assimilation capacity and lower antioxidant capacity of PP explain its more humid and nutrient-rich microhabitats (shallow soils). HHPP traits were mostly intermediate between those of HH and PP, and they allow the allotetraploid to occupy the free niche space left by the diploids.

The Essential Oil from the Resurrection Plant Myrothamnus moschatus Is Effective against Arthropods of Agricultural and Medical Interest

This work aimed to evaluate the chemical composition, insecticidal and acaricidal potential of the essential oil (EO) obtained from the resurrection plant Myrothamnus moschatus (Baill.) Baill. (Myrothamnaceae) from Madagascar. The EO bioactivity was evaluated against selected arthropod pests and vectors of agricultural and public health relevance. The most abundant volatile compounds were trans-pinocarveol (37.7 ± 4.2%) and pinocarvone (20.8 ± 3.1%), similar to the EO of the chemotype collected from the same region. Lethal concentrations (LC₅₀) or doses (LD₅₀) from acute toxicity tests were estimated for Musca domestica (L.) adults at 22.7 µg adult^-1, for Spodoptera littoralis (Boisduval) larvae at 35.6 µg larva^-1, for Culex quinquefasciatus (Say) at 43.6 µg mL^-1, for adults of Metopolophium dirhodum (Walker) at 2.4 mL L^-1, and for adults of Tetranychus urticae (Koch) at 1.2 mL L^-1. The good insecticidal and acaricidal activities determined in this work may open a new perspective on the use of this plant as a source of botanical insecticide ingredients. The exploitation of this species could also be important for the African economy, helping local farmers cultivating this plant.

In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc

Ramonda serbica Panc. is an ancient resurrection plant able to survive a long desiccation period and recover metabolic functions upon watering. The accumulation of protective late embryogenesis abundant proteins (LEAPs) is a desiccation tolerance hallmark. To propose their role in R. serbica desiccation tolerance, we structurally characterised LEAPs and evaluated LEA gene expression levels in hydrated and desiccated leaves. By integrating de novo transcriptomics and homologues LEAP domains, 318 R. serbica LEAPs were identified and classified according to their conserved motifs and phylogeny. The in silico analysis revealed that hydrophilic LEA4 proteins exhibited an exceptionally high tendency to form amphipathic α-helices. The most abundant, atypical LEA2 group contained more hydrophobic proteins predicted to fold into the defined globular domains. Within the desiccation-upregulated LEA genes, the majority encoded highly disordered DEH1, LEA1, LEA4.2, and LEA4.3 proteins, while the greatest portion of downregulated genes encoded LEA2.3 and LEA2.5 proteins. While dehydrins might chelate metals and bind DNA under water deficit, other intrinsically disordered LEAPs might participate in forming intracellular proteinaceous condensates or adopt amphipathic α-helical conformation, enabling them to stabilise desiccation-sensitive proteins and membranes. This comprehensive LEAPs structural characterisation is essential to understanding their function and regulation during desiccation aiming at crop drought tolerance improvement.

The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance

To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular "glass state". This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.

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.

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.

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

The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long-term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and targeted metabolite profiling was carried out on leaves collected from different stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 39 metabolites were differentially abundant across the different sampling points. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post-transcriptional modification in metabolic reprogramming to prepare plants for desiccation and recovery. The integrative analysis of all three data sets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of precise changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. The maintenance of cyclic electron flow and photorespiration, and the switch from C₃ to crassulacean acid metabolism photosynthesis, may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration. Transcripts with a delayed translation, ATP-independent bypasses, alternative respiratory pathway and 4-aminobutyric acid shunt may all play a role in energy management, together conferring bioenergetic advantages to meet energy demands upon rehydration. This study provides a high-resolution map of the changes occurring in primary metabolism during dehydration and rehydration and enriches our understanding of the molecular mechanisms underpinning plant desiccation tolerance. The data sets provided here will ultimately inspire biotechnological strategies for drought tolerance improvement in crops.

Transcriptome Analysis of Chloris virgata, Which Shows the Fastest Germination and Growth in the Major Mongolian Grassland Plant

Plants in Mongolian grasslands are exposed to short, dry summers and long, cold winters. These plants should be prepared for fast germination and growth activity in response to the limited summer rainfall. The wild plant species adapted to the Mongolian grassland environment may allow us to explore useful genes, as a source of unique genetic codes for crop improvement. Here, we identified the Chloris virgata Dornogovi accession as the fastest germinating plant in major Mongolian grassland plants. It germinated just 5 h after treatment for germination initiation and showed rapid growth, especially in its early and young development stages. This indicates its high growth potential compared to grass crops such as rice and wheat. By assessing growth recovery after animal bite treatment (mimicked by cutting the leaves with scissors), we found that C. virgata could rapidly regenerate leaves after being damaged, suggesting high regeneration potential against grazing. To analyze the regulatory mechanism involved in the high growth potential of C. virgata, we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis, respectively. The best-aligned sequences were annotated with gene ontology groups. When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata. Plant development is tightly regulated by phytohormones such as brassinosteroids, gibberellic acid, abscisic acid, and strigolactones. Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. We discuss the possibility that C. virgata phytohormone signaling and biosynthesis genes regulate early germination and growth advantages. Comprehensive transcriptome information will provide a useful resource for gene discovery and facilitate a deeper understanding of the diversity of the regulatory systems that have evolved in C. virgata while adapting to severe environmental conditions.

Stachyose triggers apoptotic like cell death in drought sensitive but not resilient plants

Programmed cell death (PCD) is one of the most intensively researched fields in modern mammalian biology with roles in cancer, aging, diabetes and numerous neurodegenerative diseases. It is becoming increasingly clear that PCD also plays significant roles in plant defence and responses to the environment. Given their unique ability to tolerate desiccation (cells remain viable even after they've lost 95% of their water), resurrection plants make ideal models to study the regulation of plant PCD pathways. Previously, we showed that the Australian resurrection plant, Tripogon loliiformis, suppresses plant PCD, via trehalose-mediated activation of autophagy pathways, during drying. In the present study, we created a full-length T. loliiformis cDNA library, performed a large-scale Agrobacterium screen for improved salinity tolerance and identified Stachyose synthase (TlStach) as a potential candidate for improving stress tolerance. Tripogon loliiformis shoots accumulate stachyose synthase transcripts and stachyose during drying. Attempts to generate transgenic plants expressing TlStach failed and were consistent with previous reports in mammals that demonstrated stachyose-mediated induction of apoptosis. Using a combination of transcriptomics, metabolomics and cell death assays (TUNNEL and DNA laddering), we investigated whether stachyose induces apoptotic-like cell death in T. loliiformis. We show that stachyose triggers the formation of the hallmarks of plant apoptotic-like cell death in the desiccation sensitive Nicotiana benthamiana but not the resilient T. loliiformis. These findings suggest that T. loliiformis suppresses stachyose-mediated apoptotic-like cell death and provides insights on the role of sugar metabolism and plant PCD pathways. A better understanding of how resilient plants regulate sugar metabolism and PCD pathways may facilitate future targeting of plant metabolic pathways for increased stress tolerance.

Physiological and biochemical responses involved in vegetative desiccation tolerance of resurrection plant Selaginella brachystachya

The vegetative desiccation tolerance of Selaginella brachystachya has been evaluated for its ability to revive from a desiccation (air dry) state and start normal functioning when rehydrated. In this study, S. brachystachya was identified by DNA barcoding. Experiments were conducted using the detached hydrated, desiccated and rehydrated fronds under laboratory conditions to understand the mechanism of revival upon the water availability. Scanning Electron Microscope images during desiccation showed closed stomata and inside curled leaves. Chlorophyll concentration decreased by 1.1 fold in desiccated state and recovered completely upon rehydration. However, the total carotenoid content decreased 4.5 fold while the anthocyanin concentration increased 5.98 fold and the CO2 exchange rate became negative during desiccation. Lipid peroxidation and superoxide radical production were enhanced during desiccation by 68.32 and 73.4%, respectively. Relative electrolyte leakage was found to be minimal during desiccation. Activities of antioxidant enzymes, namely peroxidase (158.33%), glutathione reductase (107.70%), catalase (92.95%) and superoxide dismutase (184.70%) were found to be higher in the desiccated state. The proline concentration increased by 1.4 fold, starch concentration decreased 3.9 fold and sucrose content increased 2.8 fold during desiccation. Upon rehydration, S. brachystachya recovered its original morphology, physiological and biochemical functions. Our results demonstrate that S. brachystachya minimizes desiccation stress through a range of morphological, physiological and biochemical mechanisms. These results provide useful insights into desiccation tolerance mechanisms for potential utilization in enhancing stress tolerance in crop plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02667-1.

Bryo-Activities: A Review on How Bryophytes Are Contributing to the Arsenal of Natural Bioactive Compounds against Fungi

Usually regarded as less evolved than their more recently diverged vascular sisters, which currently dominate vegetation landscape, bryophytes seem having nothing to envy to the defensive arsenal of other plants, since they had acquired a suite of chemical traits that allowed them to adapt and persist on land. In fact, these closest modern relatives of the ancestors to the earliest terrestrial plants proved to be marvelous chemists, as they traditionally were a popular remedy among tribal people all over the world, that exploit their pharmacological properties to cure the most different diseases. The phytochemistry of bryophytes exhibits a stunning assortment of biologically active compounds such as lipids, proteins, steroids, organic acids, alcohols, aliphatic and aromatic compounds, polyphenols, terpenoids, acetogenins and phenylquinones, thus it is not surprising that substances obtained from various species belonging to such ancestral plants are widely employed as antitumor, antipyretic, insecticidal and antimicrobial. This review explores in particular the antifungal potential of the three Bryophyta divisions-mosses (Musci), hornworts (Anthocerotae) and liverworts (Hepaticae)-to be used as a sources of interesting bioactive constituents for both pharmaceutical and agricultural areas, providing an updated overview of the latest relevant insights.

Comparative transcriptome analysis suggests convergent evolution of desiccation tolerance in Selaginella species

BACKGROUND

Desiccation tolerant Selaginella species evolved to survive extreme environmental conditions. Studies to determine the mechanisms involved in the acquisition of desiccation tolerance (DT) have focused on only a few Selaginella species. Due to the large diversity in morphology and the wide range of responses to desiccation within the genus, the understanding of the molecular basis of DT in Selaginella species is still limited.

RESULTS

Here we present a reference transcriptome for the desiccation tolerant species S. sellowii and the desiccation sensitive species S. denticulata. The analysis also included transcriptome data for the well-studied S. lepidophylla (desiccation tolerant), in order to identify DT mechanisms that are independent of morphological adaptations. We used a comparative approach to discriminate between DT responses and the common water loss response in Selaginella species. Predicted proteomes show strong homology, but most of the desiccation responsive genes differ between species. Despite such differences, functional analysis revealed that tolerant species with different morphologies employ similar mechanisms to survive desiccation. Significant functions involved in DT and shared by both tolerant species included induction of antioxidant systems, amino acid and secondary metabolism, whereas species-specific responses included cell wall modification and carbohydrate metabolism.

CONCLUSIONS

Reference transcriptomes generated in this work represent a valuable resource to study Selaginella biology and plant evolution in relation to DT. Our results provide evidence of convergent evolution of S. sellowii and S. lepidophylla due to the different gene sets that underwent selection to acquire DT.

The dehydration- and ABA-inducible germin-like protein CpGLP1 from Craterostigma plantagineum has SOD activity and may contribute to cell wall integrity during desiccation

MAIN CONCLUSION

CpGLP1 belongs to the large group of germin-like proteins and comprises a cell wall-localized protein which has superoxide dismutase activity and may contribute towards ROS metabolism and cell wall folding during desiccation. The plant cell wall is a dynamic matrix and its plasticity is essential for cell growth and processing of environmental signals to cope with stresses. A few so-called resurrection plants like Craterostigma plantagineum survive desiccation by implementing protection mechanisms. In C. plantagineum, the cell wall shrinks and folds upon desiccation to avoid mechanical and oxidative damage which contributes to cell integrity. Despite the high toxic potential, ROS are important molecules for cell wall remodeling processes as they participate in enzymatic reactions and act as signaling molecules. Here we analyzed the C. plantagineum germin-like protein 1 (CpGLP1) to understand its contribution to cell wall folding and desiccation tolerance. The analysis of the CpGLP1 sequence showed that this protein does not fit into the current GLP classification and forms a new group within the Linderniaceae. CpGLP1 transcripts accumulate in leaves in response to dehydration and ABA, and mannitol treatments transiently induce CpGLP1 transcript accumulation supporting the participation of CpGLP1 in desiccation-related processes. CpGLP1 protein from cell wall protein extracts followed transcript accumulation and protein preparations from bacteria overexpressing CpGLP1 showed SOD activity. In agreement with cell wall localization, CpGLP1 interacts with pectins which have not been reported for GLP proteins. Our data support a role for CpGLP1 in the ROS metabolism related to the control of cell wall plasticity during desiccation in C. plantagineum.

Efficient protein extraction for shotgun proteomics from hydrated and desiccated leaves of resurrection Ramonda serbica plants

Resurrection plant Ramonda serbica is a suitable model to investigate vegetative desiccation tolerance. However, the detailed study of these mechanisms at the protein level is hampered by the severe tissue water loss, high amount of phenolics and polysaccharide, and possible protein modifications and aggregations during the extraction and purification steps. When applied to R. serbica leaves, widely used protein extraction protocols containing polyvinylpolypyrrolidone and ascorbate, as well as the phenol/SDS/buffer-based protocol recommended for recalcitrant plant tissues failed to eliminate persistent contamination and ensure high protein quality. Here we compared three protein extraction approaches aiming to establish the optimal one for both hydrated and desiccated R. serbica leaves. To evaluate the efficacy of these protocols by shotgun proteomics, we also created the first R. serbica annotated transcriptome database, available at http://www.biomed.unipd.it/filearrigoni/Trinity_Sample_RT2.fasta . The detergent-free phenol-based extraction combined with dodecyl-β-D-maltoside-assisted extraction enabled high-yield and high-purity protein extracts. The phenol-based protocol improved the protein-band resolution, band number, and intensity upon electrophoresis, and increased the protein yield and the number of identified peptides and protein groups by LC-MS/MS. Additionally, dodecyl-β-D-maltoside enabled solubilisation and identification of more membrane-associated proteins. The presented study paves the way for investigating the desiccation tolerance in R. serbica, and we recommend this protocol for similar recalcitrant plant material.

Abiotic stress signalling in extremophile land plants

Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.

Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae

Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.

Transcriptome Analysis of Genes Involved in Cold Hardiness of Peach Tree (Prunus persica) Shoots during Cold Acclimation and Deacclimation

We analyzed the transcriptomes in the shoots of five-year-old 'Soomee' peach trees (Prunus persica) during cold acclimation (CA), from early CA (end of October) to late CA (middle of January), and deacclimation (DA), from late CA to late DA (middle of March), to identify the genes involved in cold hardiness. Cold hardiness of the shoots increased from early to late CA, but decreased from late CA to late DA, as indicated by decreased and increased the median lethal temperature (LT₅₀), respectively. Transcriptome analysis identified 17,208 assembled transcripts during all three stages. In total, 1891 and 3008 transcripts were differentially expressed with a |fold change| > 2 (p < 0.05) between early and late CA, and between late CA and late DA, respectively. Among them, 1522 and 2830, respectively, were functionally annotated with gene ontology (GO) terms having a greater proportion of differentially expressed genes (DEGs) associated with molecular function than biological process or cellular component categories. The biochemical pathways best represented both periods from early to late CA and from late CA to late DA were 'metabolic pathway' and 'biosynthesis of secondary metabolites'. We validated these transcriptomic results by performing reverse transcription quantitative polymerase chain reaction on the selected DEGs showing significant fold changes. The relative expressions of the selected DEGs were closely related to the LT₅₀ values of the peach tree shoots: 'Soomee' shoots exhibited higher relative expressions of the selected DEGs than shoots of the less cold-hardy 'Odoroki' peach trees. Irrespective of the cultivar, the relative expressions of the DEGs that were up- and then down-regulated during CA, from early to late CA, and DA, from late CA to late DA, were more closely correlated with cold hardiness than those of the DEGs that were down- and then up-regulated. Therefore, our results suggest that the significantly up- and then down-regulated DEGs are associated with cold hardiness in peach tree shoots. These DEGs, including early light-induced protein 1, chloroplastic, 14-kDa proline-rich protein DC2.15, glutamate dehydrogenase 2, and triacylglycerol lipase 2, could be candidate genes to determine cold hardiness.

Intertwined signatures of desiccation and drought tolerance in grasses

Grasses are among the most resilient plants, and some can survive prolonged desiccation in semiarid regions with seasonal rainfall. However, the genetic elements that distinguish grasses that are sensitive versus tolerant to extreme drying are largely unknown. Here, we leveraged comparative genomic approaches with the desiccation-tolerant grass Eragrostis nindensis and the related desiccation-sensitive cereal Eragrostis tef to identify changes underlying desiccation tolerance. These analyses were extended across C4 grasses and cereals to identify broader evolutionary conservation and divergence. Across diverse genomic datasets, we identified changes in chromatin architecture, methylation, gene duplications, and expression dynamics related to desiccation in E. nindensis It was previously hypothesized that transcriptional rewiring of seed desiccation pathways confers vegetative desiccation tolerance. Here, we demonstrate that the majority of seed-dehydration-related genes showed similar expression patterns in leaves of both desiccation-tolerant and -sensitive species. However, we identified a small set of seed-related orthologs with expression specific to desiccation-tolerant species. This supports a broad role for seed-related genes, where many are involved in typical drought responses, with only a small subset of crucial genes specifically induced in desiccation-tolerant plants.

Born to revive: molecular and physiological mechanisms of double tolerance in a paleotropical and resurrection plant

Resurrection plants recover physiological functions after complete desiccation. Almost all of them are native to tropical warm environments. However, the Gesneriaceae include four genera, remnant of the past palaeotropical flora, which inhabit temperate mountains. One of these species is additionally freezing-tolerant: Ramonda myconi. We hypothesise that this species has been able to persist in a colder climate thanks to some resurrection-linked traits. To disentangle the physiological mechanisms underpinning multistress tolerance to desiccation and freezing, we conducted an exhaustive seasonal assessment of photosynthesis (gas exchange, limitations to partitioning, photochemistry and galactolipids) and primary metabolism (through metabolomics) in two natural populations at different elevations. R. myconi displayed low rates of photosynthesis, largely due to mesophyll limitation. However, plants were photosynthetically active throughout the year, excluding a reversible desiccation period. Common responses to desiccation and low temperature involved chloroplast protection: enhanced thermal energy dissipation, higher carotenoid to Chl ratio and de-epoxidation of the xanthophyll cycle. As specific responses, antioxidants and secondary metabolic routes rose upon desiccation, while putrescine, proline and a variety of sugars rose in winter. The data suggest conserved mechanisms to cope with photo-oxidation during desiccation and cold events, while additional metabolic mechanisms may have evolved as specific adaptations to cold during recent glaciations.

Desiccation Tolerance: Avoiding Cellular Damage During Drying and Rehydration

Desiccation of plants is often lethal but is tolerated by the majority of seeds and by vegetative tissues of only a small number of land plants. Desiccation tolerance is an ancient trait, lost from vegetative tissues following the appearance of tracheids but reappearing in several lineages when selection pressures favored its evolution. Cells of all desiccation-tolerant plants and seeds must possess a core set of mechanisms to protect them from desiccation- and rehydration-induced damage. This review explores how desiccation generates cell damage and how tolerant cells assuage the complex array of mechanical, structural, metabolic, and chemical stresses and survive.Likewise, the stress of rehydration requires appropriate mitigating cellular responses. We also explore what comparative genomics, both structural and responsive, have added to our understanding of cellular protection mechanisms induced by desiccation, and how vegetative desiccation tolerance circumvents destructive, stress-induced cell senescence.

Vegetative desiccation tolerance in the resurrection plant Xerophyta humilis has not evolved through reactivation of the seed canonical LAFL regulatory network

It has been hypothesised that vegetative desiccation tolerance in resurrection plants evolved via reactivation of the canonical LAFL (i.e. LEC1, ABI3, FUS3 and LEC2) transcription factor (TF) network that activates the expression of genes during the maturation of orthodox seeds leading to desiccation tolerance of the plant embryo in most angiosperms. There is little direct evidence to support this, however, and the transcriptional changes that occur during seed maturation in resurrection plants have not previously been studied. Here we performed de novo transcriptome assembly for Xerophyta humilis, and analysed gene expression during seed maturation and vegetative desiccation. Our results indicate that differential expression of a set of 4205 genes is common to maturing seeds and desiccating leaves. This shared set of genes is enriched for gene ontology terms related to abiotic stress, including water stress and abscisic acid signalling, and includes many genes that are seed-specific in Arabidopsis thaliana and targets of ABI3. However, while we observed upregulation of orthologues of the canonical LAFL TFs and ABI5 during seed maturation, similar to what is seen in A. thaliana, this did not occur during desiccation of leaf tissue. Thus, reactivation of components of the seed desiccation program in X. humilis vegetative tissues likely involves alternative transcriptional regulators.

The Dynamic Responses of Cell Walls in Resurrection Plants During Dehydration and Rehydration

Plant cell walls define the shape of the cells and provide mechanical support. They function as osmoregulators by controlling the transport of molecules between cells and provide transport pathways within the plant. These diverse functions require a well-defined and flexible organization of cell wall components, i.e., water, polysaccharides, proteins, and other diverse substances. Cell walls of desiccation tolerant resurrection plants withstand extreme mechanical stress during complete dehydration and rehydration. Adaptation to the changing water status of the plant plays a crucial role during this process. This review summarizes the compositional and structural variations, signal transduction and changes of gene expression which occur in cell walls of resurrection plants during dehydration and rehydration.

Common and Specific Mechanisms of Desiccation Tolerance in Two Gesneriaceae Resurrection Plants. Multiomics Evidences

Environmental stress, especially water deficiency, seriously limits plant distribution and crop production worldwide. A small group of vascular angiosperm plants termed "resurrection plants," possess desiccation tolerance (DT) to withstand dehydration and to recover fully upon rehydration. In recent years, with the rapid development of life science in plants different omics technologies have been widely applied in resurrection plants to study DT. Boea hygrometrica is native in East and Southeast Asia, and Haberlea rhodopensis is endemic to the Balkans in Europe. They are both resurrection pants from Gesneriaceae family. This paper reviews recent advances in transcriptome and metabolome, and discusses the differences and similarities of DT features between both species. Finally, we believe we provide novel insights into understanding the mechanisms underlying the acquisition and evolution of desiccation tolerance of the resurrection plants that could substantially contribute to develop new approaches for agriculture to overcome water deficiency in future.

Cloning of a novel trypsin inhibitor from the Traditional Chinese medicine decoction pieces, Radix Trichosanthis

Most herbs of traditional Chinese medicine (TCM) are used as air-dried decoction pieces that are manufactured and kept at ambient temperature for long periods. Given the ability of some desiccation-tolerant plants to conserve RNA, it could be worthwhile to isolate mRNA from TCM decoction pieces as part of a transcriptomic strategy to identify new substances with potential pharmaceutical application. Here, we report the molecular cloning of a novel trypsin inhibitor (as the probable alleleic variants TKTI-2 and TKTI-3) from the decoction piece of Radix Trichosanthis, representing the dried root of Trichosanthes kirilowii. From this material, the total RNA was extracted and a cDNA library was constructed from the isolated mRNA from which the cDNAs of two precursors were successfully cloned and sequenced. TKTI-3 showed an amino-acid substitution in the otherwise highly-conserved P1-P1' reaction site of the mature peptide, which we confirmed to not be an artefact. Subsequent analysis using LC-MS/MS detected the presence of specific tryptic peptides expected from TKTI-3, confirming the presence and expression of this locus in Radix Trichosanthis. More generally, this study indicates that mRNA can persist in decoction pieces and so could present a viable option for the molecular cloning from other TCMs.

Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance

We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater diversifying selection than autosomal and organellar genes. Interestingly, this is driven primarily by divergence of male-specific genes, while divergence of other sex-linked genes is similar to autosomal genes. Through analysis of sex-specific read coverage, we identify and validate genetic sex markers for M. inflexa, which will enable diagnosis of sex for non-reproductive individuals. To investigate dehydration tolerance, we capitalized on a difference between genetic lines, which allowed us to identify multiple dehydration associated genes two of which were sex-linked, suggesting that dehydration tolerance may be impacted by sex-specific genes.

The effects of environmental light on the reorganization of chloroplasts in the resurrection of Selaginella tamariscina

Chloroplast repair and reorganization are crucial for the rehydration of resurrected plants. As one of the most important organelles in plant, photosynthesis takes place in chloroplasts. Meanwhile, light is important to the biosynthesis and activity regulation of chloroplasts. Here, we investigate the recovery of the chloroplasts and photosynthetic system in plant: Selaginella tamariscina under dark condition and environmental light (dark-light transition) condition. This study used the S. tamariscina grown in a culturing room, dehydrated S. tamariscina and S. tamariscina rehydrated in environmental light and dark conditions for 72 h as experimental material to measure and observed the chlorophyll content, chloroplast ultrastructure, photosynthesis, chlorophyll a fluorescence parameters. Specific leaf area and relative water content recovered in dark-rehydration conditions and were higher than those of light-rehydration, while dark-rehydration did not fully recover the chlorophyll content, net photosynthetic rate, water-use efficiency, nor the Fv/Fm. Dehydration did not destroy the chloroplast envelop, but increased the number of plastoglobules and disturbed the granum structure. As a homeochlorophyllous resurrection plant, reorganization, not the rebuilding of chloroplasts, occurs during the dehydration and rehydration processes in S. tamariscina. Environmental light signals play an important role in the recovery of photosynthetic systems.

Desiccation tolerance in plants: Structural characterization of the cell wall hemicellulosic polysaccharides in three Selaginella species

Drought-induced dehydration of vegetative tissues in lycopods affects growth and survival. Different species of Selaginella have evolved a series of specialized mechanisms to tolerate desiccation in vegetative tissues in response to water stress. In the present study, we report on the structural characterization of the leaf cell wall of the desiccation-tolerant species S. involvens and two desiccation-sensitive species, namely S. kraussiana and S. moellendorffii. Isolated cell walls from hydrated and desiccated leaves of each species were fractionated and the resulting oligosaccharide fragments were analyzed to determine their structural features. Our results demonstrate that desiccation induces substantial modifications in the cell wall composition and structure. Altogether, these data highlight the fact that structural remodeling of cell wall hemicellulosic polysaccharides including XXXG-rich xyloglucan, arabinoxylan and acetylated galactomannan is an important process in order to mitigate desiccation stress in Selaginella.

Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

BACKGROUND

Water shortage is a major factor that harms agriculture and ecosystems worldwide. Plants display various levels of tolerance to water deficit, but only resurrection plants can survive full desiccation of their vegetative tissues. Haberlea rhodopensis, an endemic plant of the Balkans, is one of the few resurrection plants found in Europe. We performed transcriptomic analyses of this species under slight, severe and full dehydration and recovery to investigate the dynamics of gene expression and associate them with existing physiological and metabolomics data.

RESULTS

De novo assembly yielded a total of 142,479 unigenes with an average sequence length of 1034 nt. Among them, 18,110 unigenes were differentially expressed. Hierarchical clustering of all differentially expressed genes resulted in seven clusters of dynamic expression patterns. The most significant expression changes, involving more than 15,000 genes, started at severe dehydration (~ 20% relative water content) and were partially maintained at full desiccation (< 10% relative water content). More than a hundred pathways were enriched and functionally organized in a GO/pathway network at the severe dehydration stage. Transcriptomic changes in key pathways were analyzed and discussed in relation to metabolic processes, signal transduction, quality control of protein and DNA repair in this plant during dehydration and rehydration.

CONCLUSION

Reprograming of the transcriptome occurs during severe dehydration, resulting in a profound alteration of metabolism toward alternative energy supply, hormone signal transduction, and prevention of DNA/protein damage under very low cellular water content, underlying the observed physiological and metabolic responses and the resurrection behavior of H. rhodopensis.

Functional characterization of galactinol synthase and raffinose synthase in desiccation tolerance acquisition in developing Arabidopsis seeds

Raffinose family oligosaccharides (RFOs) accumulate during seed development, and have been thought to be associated with the acquisition of desiccation tolerance (DT) by seeds. Here, comprehensive approaches were adopted to evaluate the changes of DT in developing Arabidopsis seeds of wild type, overexpression (OX-AtGS1/GS2/RS5), and mutant lines by manipulating the expression levels of the GALACTINOL SYNTHASE (GS) and RAFFINOSE SYNTHASE (RS) genes. Our results indicate that seeds of the double mutant (gs1, gs2) and rs5 delayed the timing of DT acquisition as compared to wild type. Subsequent detection confirmed that seeds from OX-AtGS1/GS2 plants with high levels of galactinol, raffinose, and stachyose, and OX-AtRS5 plants possess more raffinose and stachyose but less galactinol compared to wild type. These lines all showed greater germination percentage and shorter time to 50% germination after desiccation treatment at 11 and 15 days after flower (DAF). Further analysis revealed that the role of RFOs is time limited and mainly affects the middle stage (9-16 DAF) of seed development by enhancing seed viability and the ratio of GSH to GSSH in cells, but there is no significant difference in DT of mature seeds. In addition, RFOs could reduce damage to seeds caused by oxidative stress. We conclude that GALACTINOL SYNTHASE and RAFFINOSE SYNTHASE play important roles in DT acquisition during Arabidopsis seed development, and that galactinol and RFOs are crucial protective compounds in the response of seeds to desiccation stress.

PtDRG1, a Desiccation Response Gene from Pyropia tenera (Rhodophyta), Exhibits Chaperone Function and Enhances Abiotic Stress Tolerance

Pyropia are commercially valuable marine red algae that grow in the intertidal zone. They are extremely tolerant to desiccation stress. We have previously identified and reported desiccation response genes (DRGs) based on transcriptome analysis of P. tenera. Among them, PtDRG1 encodes a polypeptide of 22.6 kDa that is located in the chloroplast. PtDRG1 does not share sequence homology with any known gene deposited in public database. Transcription of PtDRG1 gene was upregulated by osmotic stress induced by mannitol or H₂O₂ as well as desiccation stress, but not by heat. When PtDRG1 was overexpressed in Escherichia coli or Chlamydomonas, transformed cells grew much better than control cells under high temperature as well as osmotic stress induced by mannitol and NaCl. In addition, PtDRG1 significantly reduced thermal aggregation of substrate protein under heat stress condition. These results demonstrate that PtDRG1 has a chaperone function and plays a role in tolerance mechanism for abiotic stress. This study shows that red algae have unknown stress proteins such as PtDRG1 that contributes to stress tolerance.

Gene expression profiles of Pyropia yezoensis in response to dehydration and rehydration stresses

Pyropia yezoensis is an economically important marine macroalgae, naturally distributed in the upper intertidal zone. Owing to the nature of its habitat, the thallus will periodically be exposed to seawater or atmosphere, and can lose up to 95% of its cellular water content. This makes the alga an ideal research model to investigate the mechanisms of desiccation tolerance. In this study, we investigated the response mechanisms to dehydration and rehydration stresses at the transcription level in Pyropia yezoensis. The differently expressed genes were analyzed based on the different functions of encoding proteins: effector proteins (chloroplast proteins, macromolecular protective substances, and toxicity degradation enzymes) and regulatory proteins (protein kinases and phosphatases). Under osmotic stress, the unigenes related to photosynthesis were down-regulated significantly while those encoding glutathione transferase, superoxide dismutase and heat shock proteins were up-regulated significantly. We inferred that the photosynthetic activity was reduced to prevent damage caused by photosynthetic by-products and that the expression of antioxidant enzyme was increased to prevent the damage associated with reactive oxygen species. Additionally, unigenes encoding serine/threonine kinases and phospholipases were up-regulated in response to osmotic stress, indicating that these kinases play an important role in osmotolerance. Our work will serve as an essential foundation for the understanding of desiccation tolerance mechanisms in Pyropia yezoensis in the upper intertidal zones of rocky coasts.

Biochemical responses of the desiccation-tolerant resurrection fern Pleopeltis polypodioides to dehydration and rehydration

The epiphytic fern Pleopeltis polypodioides can tolerate repeated drying and rehydration events without conspicuous damage. To understand the biochemical principles of drought-tolerance, we analyzed the effect of dehydration and rehydration at 25 °C on hydroperoxide and lipid hydroperoxide, the activities of antioxidative (catalase and glutathione-oxidizing) enzymes and evaluated changes in fatty acid composition and saturation levels. Dehydration increased peroxide concentration and the activity of glutathione oxidases, but reduced catalase activity. During dehydration, the biosynthesis of palmitic (C16:0), linoleic (C18:2), linolenic (C18:3) and stearic acid (C18:0) increased 18, 12, 20, and 8-fold, respectively. In contrast, rehydration lowered levels of peroxides, the activity of glutathione-oxidizing enzymes, and fatty acids but increased catalase activity. The coordinated changes during de- and rehydration suggest that lipids and oxidative and antioxidative enzymes are components of the drought-resistance system.

ABA regulation of antioxidant activity during post-germination desiccation and subsequent rehydration in wheat

ABA regulation of antioxidant activity during post-germination desiccation and subsequent rehydration was studied in two wheat cultivars PBW 644 (ABA-higher sensitive and drought tolerant) and PBW 343 (ABA-lesser sensitive and drought susceptible) where 1 d-germinated seeds were exposed to ABA/ PEG- 6000 for next 1 d, desiccated for 4 d and subsequently rehydrated for 4 d. Ascorbate, dehydrascorbate to ascorbate ratio, malondialdehyde (MDA), hydroxyl radicals, and activities of monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), alcohol dehydrogenase (AlcDH) and aldehyde dehydrogenase (AldDH) were measured in seedlings just before desiccation (2 d old), desiccated (6 d old) and rehydrated (10 d old) stages. ROS/NO signaling was studied under CT and ABA supply by supplying ROS and NO scavengers. During desiccation, both cultivars showed increase of oxidative stress (dehydroascorbate to ascorbate ratio, MDA, hydroxyl radicals) and antioxidant activity in the form of ascorbate content and AldDH activity while other antioxidant enzymes were not increased. PBW 644 showed higher antioxidant activity thus produced less oxidative stress compared to PBW 343. During rehydration, activities of all antioxidant enzymes and levels of ROS (hydroxyl radicals) were increased in both cultivars and MDA was decreased in PBW 343. ABA supply improved desiccation as well as rehydration by improving all parameters of antioxidant activity tested in this study. PEG supply resembled to ABA-supply for its effects. ABA/PEG improvements were seen higher in PBW 644. ROS/NO-signalling was involved under CT as well as under ABA for increasing antioxidant activity during desiccation as well as rehydration in both cultivars.

Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis

Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.

Protection of photosynthesis in desiccation-tolerant resurrection plants

Inhibition of photosynthesis is a central, primary response that is observed in both desiccation-tolerant and desiccation-sensitive plants affected by drought stress. Decreased photosynthesis during drought stress can either be due to the limitation of carbon dioxide entry through the stomata and the mesophyll cells, due to increased oxidative stress or due to decreased activity of photosynthetic enzymes. Although the photosynthetic rates decrease in both desiccation-tolerant and sensitive plants during drought, the remarkable difference lies in the complete recovery of photosynthesis after rehydration in desiccation-tolerant plants. Desiccation of sensitive plants leads to irreparable damages of the photosynthetic membranes, in contrast the photosynthetic apparatus is deactivated during desiccation in desiccation-tolerant plants. Desiccation-tolerant plants employ different strategies to protect and/or maintain the structural integrity of the photosynthetic apparatus to reactivate photosynthesis upon water availability. Two major mechanisms are distinguished. Homoiochlorophyllous desiccation-tolerant plants preserve chlorophyll and thylakoid membranes and require active protection mechanisms, while poikilochlorophyllous plants degrade chlorophyll in a regulated manner but then require de novo synthesis during rehydration. Desiccation-tolerant plants, particularly homoiochlorophyllous plants, employ conserved and novel antioxidant enzymes/metabolites to minimize the oxidative damage and to protect the photosynthetic machinery. De novo synthesized, stress-induced proteins in combination with antioxidants are localized in chloroplasts and are important components of the protective network. Genome sequence informations provide some clues on selection of genes involved in protecting photosynthetic structures; e.g. ELIP genes (early light inducible proteins) are enriched in the genomes and more abundantly expressed in homoiochlorophyllous desiccation-tolerant plants. This review focuses on the mechanisms that operate in the desiccation-tolerant plants to protect the photosynthetic apparatus during desiccation.

Analysis of pcC13-62 promoters predicts a link between cis-element variations and desiccation tolerance in Linderniaceae

Reproductive structures of plants (e.g. seeds) and vegetative tissues of resurrection plants can tolerate desiccation. Many genes encoding desiccation-related proteins (DRPs) have been identified in the resurrection plant Craterostigma plantagineum, but the function of these genes remains mainly hypothetical. Here, the importance of the DRP gene pcC13-62 for desiccation tolerance is evaluated by analysing its expression in C. plantagineum and in the closely related desiccation-tolerant species Lindernia brevidens and the desiccation-sensitive species Lindernia subracemosa. Quantitative analysis revealed that pcC13-62 transcripts accumulate at a much lower level in desiccation-sensitive species than in desiccation-tolerant species. The study of pcC13-62 promoters from these species demonstrated a correlation between promoter activity and gene expression levels, suggesting transcriptional regulation of gene expression. Comparison of promoter sequences identified a dehydration-responsive element motif in the promoters of tolerant species that is required for dehydration-induced β-glucuronidase (GUS) accumulation. We hypothesize that variations in the regulatory sequences of the pcC13-62 gene occurred to establish pcC13-62 expression in vegetative tissues, which might be required for desiccation tolerance. The pcC13-62 promoters could also be activated by salt stress in Arabidopsis thaliana plants stably transformed with promoter::GUS constructs.

Molecular responses to dehydration and desiccation in desiccation-tolerant angiosperm plants

Due to the ability to tolerate extreme dehydration, desiccation-tolerant plants have been widely investigated to find potential approaches for improving water use efficiency or developing new crop varieties. The studies of desiccation-tolerant plants have identified sugar accumulation, specific protein synthesis, cell structure changes, and increased anti-oxidative reactions as part of the mechanisms of desiccation tolerance. However, plants respond differently according to the severity of water loss, and the process of water loss affects desiccation tolerance. A detailed analysis within the dehydration process is important for understanding the process of desiccation tolerance. This review defines dehydration and desiccation, finds the boundary for the relative water content between dehydration and desiccation, compares the molecular responses to dehydration and desiccation, compares signaling differences between dehydration and desiccation, and finally summarizes the strategies launched in desiccation-tolerant plants for dehydration and desiccation, respectively. The roles of abscisic acid (ABA) and reactive oxygen species (ROS) in sensing and signaling during dehydration are discussed. We outline how this knowledge can be exploited to generate drought-tolerant crop plants.

Plant Life in Extreme Environments: How Do You Improve Drought Tolerance?

Systems studies of drought stress in resurrection plants and other xerophytes are rapidly identifying a large number of genes, proteins and metabolites that respond to severe drought stress or desiccation. This has provided insight into drought resistance mechanisms, which allow xerophytes to persist under such extreme environmental conditions. Some of the mechanisms that ensure cellular protection during severe dehydration appear to be unique to desert species, while many other stress signaling pathways are in common with well-studied model and crop species. However, despite the identification of many desiccation inducible genes, there are few "gene-to-field" examples that have led to improved drought tolerance and yield stability derived from resurrection plants, and only few examples have emerged from model species. This has led to many critical reviews on the merit of the experimental approaches and the type of plants used to study drought resistance mechanisms. This article discusses the long-standing arguments between the ecophysiology and molecular biology communities, on how to "drought-proof" future crop varieties. It concludes that a more positive and inclusive dialogue between the different disciplines is needed, to allow us to move forward in a much more constructive way.

Dehydration survival of crop plants and its measurement

Dehydration survival under drought stress is defined in this review as the transition from plant activity into a quiescent state of life preservation, which will be terminated by either recovery or death, depending on the stress regime and the plant's resilience. Dehydration survival is a popular phenotype by which functional genomics attempts to test gene function in drought resistance and survival. The available reports on phenotyping and genotyping of dehydration survival in genomic studies indicate that the measurement of this trait is often biased to the extent that misguided interpretations are likely to occur. This review briefly discusses the physiological basis of dehydration survival in resurrection plants and crop plants, and concludes that in phenotyping dehydration survival there is a need to distinguish between dehydration avoidance and dehydration tolerance (also termed desiccation tolerance) in affecting survival and recovery. Without this distinction, functional genomics studies of the trait might be biased. Survival due to dehydration avoidance is expressed by the capacity to maintain a relatively high plant water status as the plant is desiccated. Survival due to dehydration tolerance is expressed by delayed mortality (mortality at a relatively low plant water status) as affected by the resilience of plant metabolism. The common test of dehydration survival, using the relative recovery after a given number of stress days, is therefore insufficient because it is mainly driven by dehydration avoidance and so ignores a possible role for dehydration tolerance. Conceivable methods for more accurate phenotyping of the two components of dehydration survival are proposed and discussed.

An osmotin from the resurrection plant Tripogon loliiformis (TlOsm) confers tolerance to multiple abiotic stresses in transgenic rice

Osmotin is a key protein associated with abiotic and biotic stress response in plants. In this study, an osmotin from the resurrection plant Tripogon loliiformis (TlOsm) was characterized and functionally analyzed under abiotic stress conditions in T. loliiformis as well as in transgenic Nicotiana tabacum (tobacco) and Oryza sativa (rice) plants. Real-time PCR analysis on mixed elicitor cDNA libraries from T. loliiformis showed that TlOsm was upregulated a 1000-fold during the early stages of osmotic stresses (cold, drought, and salinity) in both shoots and roots but downregulated in shoots during heat stress. There was no change in TlOsm gene expression in roots of heat-stressed plants and during plant development. The plasma membrane localization of TlOsm was showed in fluorescent-tagged TlOsm tobacco plants using confocal laser scanning microscopic analysis. Transgenic rice plants expressing TlOsm were assessed for enhanced tolerance to salinity, drought and cold stresses. Constitutively expressed TlOsm in transgenic rice plants showed increased tolerance to cold, drought and salinity stress when compared with the wild-type and vector control counterparts. This was evidenced by maintained growth, retained higher water content and membrane integrity, and improved survival rate of TlOsm-expressing plants. The results thus indicate the involvement of TlOsm in plant response to multiple abiotic stresses, possibly through the signaling pathway, and highlight its potential applications for engineering crops with improved tolerance to cold, drought and salinity stress.

Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum

Resurrection plants desiccate during periods of prolonged drought stress, then resume normal cellular metabolism upon water availability. Desiccation tolerance has multiple origins in flowering plants, and it likely evolved through rewiring seed desiccation pathways. Oropetium thomaeum is an emerging model for extreme drought tolerance, and its genome, which is the smallest among surveyed grasses, was recently sequenced. Combining RNA-seq, targeted metabolite analysis and comparative genomics, we show evidence for co-option of seed-specific pathways during vegetative desiccation. Desiccation-related gene co-expression clusters are enriched in functions related to seed development including several seed-specific transcription factors. Across the metabolic network, pathways involved in programmed cell death inhibition, ABA signalling and others are activated during dehydration. Oleosins and oil bodies that typically function in seed storage are highly abundant in desiccated leaves and may function for membrane stability and storage. Orthologs to seed-specific LEA proteins from rice and maize have neofunctionalized in Oropetium with high expression during desiccation. Accumulation of sucrose, raffinose and stachyose in drying leaves mirrors sugar accumulation patterns in maturing seeds. Together, these results connect vegetative desiccation with existing seed desiccation and drought responsive pathways and provide some key candidate genes for engineering improved drought tolerance in crop plants.

Angiosperm Plant Desiccation Tolerance: Hints from Transcriptomics and Genome Sequencing

Desiccation tolerance (DT) in angiosperms is present in the small group of resurrection plants and in seeds. DT requires the presence of protective proteins, specific carbohydrates, restructuring of membrane lipids, and regulatory mechanisms directing a dedicated gene expression program. Many components are common to resurrection plants and seeds; however, some are specific for resurrection plants. Understanding how each component contributes to DT is challenging. Recent transcriptome analyses and genome sequencing indicate that increased expression is essential of genes encoding protective components, recently evolved, species-specific genes and non-protein-coding RNAs. Modification and reshuffling of existing cis-regulatory promoter elements seems to play a role in the rewiring of regulatory networks required for increased expression of DT-related genes in resurrection species.

The Arabidopsis Phytocystatin AtCYS5 Enhances Seed Germination and Seedling Growth under Heat Stress Conditions

Phytocystatins (PhyCYSs) are plant-specific proteinaceous inhibitors that are implicated in protein turnover and stress responses. Here, we characterized a PhyCYS from Arabidopsis thaliana, which was designated AtCYS5. RT-qPCR analysis showed that the expression of AtCYS5 in germinating seeds was induced by heat stress (HS) and exogenous abscisic acid (ABA) treatment. Analysis of the expression of the β-glucuronidase reporter gene under the control of the AtCYS5 promoter showed that AtCYS5 expression during seed germination was induced by HS and ABA. Constitutive overexpression of AtCYS5 driven by the cauliflower mosaic virus 35S promoter led to enhanced HS tolerance in transgenic Arabidopsis, which was characterized by higher fresh weight and root length compared to wild-type (WT) and knockout (cys5) plants grown under HS conditions. The HS tolerance of At-CYS5-overexpressing transgenic plants was associated with increased insensitivity to exogenous ABA during both seed germination and post-germination compared to WT and cys5. Although no HS elements were identified in the 5'-flanking region of AtCYS5, canonical ABA-responsive elements (ABREs) were detected. AtCYS5 was upregulated in ABA-treated protoplasts transiently co-expressing this gene and genes encoding bZIP ABRE-binding factors (ABFs and AREB3). In the absence of ABA, ABF1 and ABF3 directly bound to the ABREs in the AtCYS5 promoter, which activated the transcription of this gene in the presence of ABA. These results suggest that an ABA-dependent pathway plays a positive role in the HS-responsive expression of AtCYS5 during seed germination and post-germination growth.

Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China

BACKGROUND

Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown. Based on transcriptomic analyses, polymorphic EST-SSR (simple sequence repeats in expressed sequence tags) molecular primers can be designed, which will greatly facilitate further investigations of the population genetics and demographic histories of DT plants.

METHODS

In the present study, we used the platform Illumina HiSeq™2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information, the EST-SSR markers were developed, and the functional annotation of ESTs containing polymorphic SSRs were obtained through BLASTX.

RESULTS

A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to the known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to Gene Ontology (GO) classifications and Cluster of Orthologous Groups (COG), respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were concentrated on dinucleotides, pentanucleotides and hexanucleotides. Finally, 17 pairs with stable, highly polymorphic loci were selected for polymorphism screening. There was a total of 65 alleles, with 2-6 alleles at each locus. Primarily due to the unique biological characteristics of plants, the HE (0-0.196), HO (0.082-0.14) and PIC (0-0.155) per locus were very low. The functional annotation distribution centered on ESTs containing di- and tri-nucleotide SSRs, and the ESTs containing primers BC2, BC4 and BC12 were annotated to vegetative dehydration/desiccation pathways.

DISCUSSION

This work is the first genetic study of B. clarkeana as a new plant resource of DT genes. A substantial number of transcriptome sequences were generated in this study. These sequences are valuable resources for gene annotation and discovery as well as molecular marker development. These sequences could also provide a valuable basis for future molecular studies of B. clarkeana.

Modulating role of ROS in re-establishing desiccation tolerance in germinating seeds of Caragana korshinskii Kom

In close agreement with visible germination, orthodox seeds lose desiccation tolerance (DT). This trait can be regained under osmotic stress, but the mechanisms are poorly understood. In this study, germinating seeds of Caragana korshinskii Kom. were investigated, focusing on the potential modulating roles of reactive oxygen species (ROS) in the re-establishment of DT. Germinating seeds with 2 mm long radicles can be rendered tolerant to desiccation by incubation in a polyethylene glycol (PEG) solution (-1.7 MPa). Upon PEG incubation, ROS accumulation was detected in the radicles tip by nitroblue tetrazolium chloride staining and further confirmed by confocal microscopy. The PEG-induced re-establishment of DT was repressed when ROS scavengers were added to the PEG solution. Moreover, ROS act downstream of abscisic acid (ABA) to modulate PEG-mediated re-establishment of DT and serve as a new inducer to re-establish DT. Transcriptomic analysis revealed that re-establishment of DT by ROS involves the up-regulation of key genes in the phenylpropanoid-flavonoid pathway, and total flavonoid content and key enzyme activity increased after ROS treatment. Furthermore, DT was repressed by an inhibitor of phenylalanine ammonia lyase. Our data suggest that ROS play a key role in the re-establishment of DT by regulating stress-related genes and the phenylpropanoid-flavonoid pathway.