A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Induced Expression of Xerophyta viscosa XvSap1 Gene Enhances Drought Tolerance in Transgenic Sweet Potato

Drought stress often leads to reduced yields and is a perilous delimiter for expanded cultivation and increased productivity of sweet potato. Cell wall stabilization proteins have been identified to play a pivotal role in mechanical stabilization during desiccation stress mitigation in plants. They are involved in numerous cellular processes that modify cell wall properties to tolerate the mechanical stress during dehydration. This provides a plausible approach to engineer crops for enhanced stable yields under adverse climatic conditions. In this study, we genetically engineered sweet potato cv. Jewel with XvSap1 gene encoding a protein related to cell wall stabilization, isolated from the resurrection plant Xerophyta viscosa, under stress-inducible XvPSap1 promoter via Agrobacterium-mediated transformation. Detection of the transgene by PCR, Southern blot, and quantitative real-time PCR (qRT-PCR) analyses revealed the integration of XvSap1 in the three independent events. Phenotypic evaluation of shoot length, number of leaves, and yield revealed that the transgenic plants grew better than the wild-type plants under drought stress. Assessment of biochemical indices during drought stress showed higher levels of chlorophyll, free proline, and relative water content and decreased lipid peroxidation in transgenic plants than in wild types. Our findings demonstrate that XvSap1 enhances drought tolerance in transgenic sweet potato without causing deleterious phenotypic and yield changes. The transgenic drought-tolerant sweet potato lines provide a valuable resource as a drought-tolerant crop on arid lands of the world.

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation

Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginellamoellendorffii. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress.

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.

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

PREMISE

We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships.

METHODS

Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent-based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species.

RESULTS

The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm-wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives.

DISCUSSION

Our customized panel reliably retrieves targeted loci from Dioscorea, is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.

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.

Roots of the Resurrection Plant Tripogon loliiformis Survive Desiccation Without the Activation of Autophagy Pathways by Maintaining Energy Reserves

Being sessile, plants must regulate energy balance, potentially via source-sink relations, to compromise growth with survival in stressful conditions. Crops are sensitive, possibly because they allocate their energy resources toward growth and yield rather than stress tolerance. In contrast, resurrection plants tightly regulate sugar metabolism and use a series of physiological adaptations to suppress cell death in their vegetative tissue to regain full metabolic capacity from a desiccated state within 72 h of watering. Previously, we showed that shoots of the resurrection plant Tripogon loliiformis, initiate autophagy upon dehydration as one strategy to reinstate homeostasis and suppress cell death. Here, we describe the relationship between energy status, sugar metabolism, trehalose-mediated activation of autophagy pathways and investigate whether shoots and roots utilize similar desiccation tolerance strategies. We show that despite containing high levels of trehalose, dehydrated Tripogon roots do not display elevated activation of autophagy pathways. Using targeted and non-targeted metabolomics, transmission electron microscopy (TEM) and transcriptomics we show that T. loliiformis engages a strategy similar to the long-term drought responses of sensitive plants and continues to use the roots as a sink even during sustained stress. Dehydrating T. loliiformis roots contained more sucrose and trehalose-6-phosphate compared to shoots at an equivalent water content. The increased resources in the roots provides sufficient energy to cope with stress and thus autophagy is not required. These results were confirmed by the absence of autophagosomes in roots by TEM. Upregulation of sweet genes in both shoots and roots show transcriptional regulation of sucrose translocation from leaves to roots and within roots during dehydration. Differences in the cell's metabolic status caused starkly different cell death responses between shoots and roots. These findings show how shoots and roots utilize different stress response strategies and may provide candidate targets that can be used as tools for the improvement of stress tolerance in crops.

Genome-level responses to the environment: plant desiccation tolerance

Plants being sessile organisms are well equipped genomically to respond to environmental stressors peculiar to their habitat. Evolution of plants onto land was enabled by the ability to tolerate extreme water loss (desiccation), a feature that has been retained within genomes but not universally expressed in most land plants today. In the majority of higher plants, desiccation tolerance (DT) is expressed only in reproductive tissues (seeds and pollen), but some 135 angiosperms display vegetative DT. Here, we review genome-level responses associated with DT, pointing out common and yet sometimes discrepant features, the latter relating to evolutionary adaptations to particular niches. Understanding DT can lead to the ultimate production of crops with greater tolerance of drought than is currently realized.

Dissecting the Genomic Diversification of Late Embryogenesis Abundant (LEA) Protein Gene Families in Plants

Late embryogenesis abundant (LEA) proteins include eight multigene families that are expressed in response to water loss during seed maturation and in vegetative tissues of desiccation tolerant species. To elucidate LEA proteins evolution and diversification, we performed a comprehensive synteny and phylogenetic analyses of the eight gene families across 60 complete plant genomes. Our integrated comparative genomic approach revealed that synteny conservation and diversification contributed to LEA family expansion and functional diversification in plants. We provide examples that: 1) the genomic diversification of the Dehydrin family contributed to differential evolution of amino acid sequences, protein biochemical properties, and gene expression patterns, and led to the appearance of a novel functional motif in angiosperms; 2) ancient genomic diversification contributed to the evolution of distinct intrinsically disordered regions of LEA_1 proteins; 3) recurrent tandem-duplications contributed to the large expansion of LEA_2; and 4) dynamic synteny diversification played a role on the evolution of LEA_4 and its function on plant desiccation tolerance. Taken together, these results show that multiple evolutionary mechanisms have not only led to genomic diversification but also to structural and functional plasticity among LEA proteins which have jointly contributed to the adaptation of plants to water-limiting environments.

A brief history of thylakoid biogenesis

The thylakoid membrane network inside chloroplasts harbours the protein complexes that are necessary for the light-dependent reactions of photosynthesis. Cellular processes for building and altering this membrane network are therefore essential for life on Earth. Nevertheless, detailed molecular processes concerning the origin and synthesis of the thylakoids remain elusive. Thylakoid biogenesis is strongly coupled to the processes of chloroplast differentiation. Chloroplasts develop from special progenitors called proplastids. As many of the needed building blocks such as lipids and pigments derive from the inner envelope, the question arises how these components are recruited to their target membrane. This review travels back in time to the beginnings of thylakoid membrane research to summarize findings, facts and fictions on thylakoid biogenesis and structure up to the present state, including new insights and future developments in this field.

DNA synthesis pattern, proteome, and ABA and GA signalling in developing seeds of Norway maple (Acer platanoides)

Mature seeds of Norway maple exhibit desiccation tolerance and deep physiological dormancy. Flow cytometry, proteomics, and immunodetection have been combined to investigate seed development of this species. DNA content analysis revealed that cell cycle/endoreduplication activity differs between seed organs and developmental stages. In the embryo axis, the proportion of the nuclei with the highest DNA content (4C) increases at the beginning of maturation (17 weeks after flowering; WAF), and then is stable until the end of maturation, to increase again after drying. In cotyledons, during maturation endopolyploid nuclei (8C) occur and the intensity of endoreduplication increases up to 21 WAF, and then is stable until development is completed. In dry mature seeds, the proportion of 4C nuclei is high, and reaches 36% in the embryo axis and 52% in cotyledons. Proteomic studies revealed that energy and carbon metabolism, fatty acid biosynthesis, storage and antioxidant proteins are associated with seed development. Study of the ABI5 protein, a transcription factor involved in ABA signalling, and the RGL2 protein, a repressor of the GA signalling indicates that the highest accumulation of these proteins occurs in fully-matured and dried seeds. It is suggested that this increase in accumulation can be associated with completion of maturation, mainly with desiccation and dormancy acquisition.

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.

Developing naturally stress-resistant crops for a sustainable agriculture

A major problem facing humanity is that our numbers are growing but the availability of land and fresh water for agriculture is not. This problem is being exacerbated by climate change-induced increases in drought, and other abiotic stresses. Stress-resistant crops are needed to ensure yield stability under stress conditions and to minimize the environmental impacts of crop production. Evolution has created thousands of species of naturally stress-resistant plants (NSRPs), some of which have already been subjected to human domestication and are considered minor crops. Broader cultivation of these minor crops will diversify plant agriculture and the human diet, and will therefore help improve global food security and human health. More research should be directed toward understanding and utilizing NSRPs. Technologies are now available that will enable researchers to rapidly improve the genetics of NSRPs, with the goal of increasing NSRP productivity while retaining NSRP stress resistance and nutritional value.

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets

Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses. Overall, changes at the transcriptional level were reflected in plant spectral traits amenable to field-level physiological measurements, although changes in photosynthesis-related pathways were found likely to be under more complex post-transcriptional control. Examining homoeologous genes with a 1:1:1 relationship across the A, B, and D genomes (triads), we revealed a complex genomic architecture for drought responses under field conditions, involving gene homoeolog specialization, multiple gene clusters, gene families, miRNAs, and transcription factors coordinating these responses. Our results provide a new focus for genomics-assisted breeding of drought-tolerant wheat cultivars.

A chromosome-scale assembly of the model desiccation tolerant grass Oropetium thomaeum

Oropetium thomaeum is an emerging model for desiccation tolerance and genome size evolution in grasses. A draft genome of Oropetium was recently sequenced, but the lack of a chromosome-scale assembly has hindered comparative analyses and downstream functional genomics. Here, we reassembled Oropetium, and anchored the genome into 10 chromosomes using high-throughput chromatin conformation capture (Hi-C) based chromatin interactions. A combination of high-resolution RNAseq data and homology-based gene prediction identified thousands of new, conserved gene models that were absent from the V1 assembly. This includes thousands of new genes with high expression across a desiccation timecourse. Comparison between the Sorghum and Oropetium genomes revealed a surprising degree of chromosome-level collinearity, and several chromosome pairs have near perfect synteny. Other chromosomes are collinear in the gene rich chromosome arms but have experienced pericentric translocations. Together, these resources will be useful for the grass-comparative genomic community and further establish Oropetium as a model resurrection plant.

A chromosome-scale assembly of the model desiccation tolerant grass Oropetium thomaeum

Oropetium thomaeum is an emerging model for desiccation tolerance and genome size evolution in grasses. A draft genome of Oropetium was recently sequenced, but the lack of a chromosome-scale assembly has hindered comparative analyses and downstream functional genomics. Here, we reassembled Oropetium, and anchored the genome into 10 chromosomes using high-throughput chromatin conformation capture (Hi-C) based chromatin interactions. A combination of high-resolution RNAseq data and homology-based gene prediction identified thousands of new, conserved gene models that were absent from the V1 assembly. This includes thousands of new genes with high expression across a desiccation timecourse. Comparison between the Sorghum and Oropetium genomes revealed a surprising degree of chromosome-level collinearity, and several chromosome pairs have near perfect synteny. Other chromosomes are collinear in the gene rich chromosome arms but have experienced pericentric translocations. Together, these resources will be useful for the grass-comparative genomic community and further establish Oropetium as a model resurrection plant.

Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.)

Plants respond to drought stress through the ABA dependent and independent pathways, which in turn modulate transcriptional regulatory hubs. Here, we employed Illumina RNA-Seq to analyze a total of 18 cDNA libraries from leaves, sap, and roots of papaya plants under drought stress. Reference and de novo transcriptomic analyses identified 8,549 and 6,089 drought-responsive genes and unigenes, respectively. Core sets of 6 and 34 genes were simultaneously up- or down-regulated, respectively, in all stressed samples. Moreover, GO enrichment analysis revealed that under moderate drought stress, processes related to cell cycle and DNA repair were up-regulated in leaves and sap; while responses to abiotic stress, hormone signaling, sucrose metabolism, and suberin biosynthesis were up-regulated in roots. Under severe drought stress, biological processes related to abiotic stress, hormone signaling, and oxidation-reduction were up-regulated in all tissues. Moreover, similar biological processes were commonly down-regulated in all stressed samples. Furthermore, co-expression network analysis revealed three and eight transcriptionally regulated modules in leaves and roots, respectively. Seventeen stress-related TFs were identified, potentially serving as main regulatory hubs in leaves and roots. Our findings provide insight into the molecular responses of papaya plant to drought, which could contribute to the improvement of this important tropical crop.

Plant Desiccation Tolerance and its Regulation in the Foliage of Resurrection “Flowering-Plant” Species

The majority of flowering-plant species can survive complete air-dryness in their seed and/or pollen. Relatively few species (‘resurrection plants’) express this desiccation tolerance in their foliage. Knowledge of the regulation of desiccation tolerance in resurrection plant foliage is reviewed. Elucidation of the regulatory mechanism in resurrection grasses may lead to identification of genes that can improve stress tolerance and yield of major crop species. Well-hydrated leaves of resurrection plants are desiccation-sensitive and the leaves become desiccation tolerant as they are drying. Such drought-induction of desiccation tolerance involves changes in gene-expression causing extensive changes in the complement of proteins and the transition to a highly-stable quiescent state lasting months to years. These changes in gene-expression are regulated by several interacting phytohormones, of which drought-induced abscisic acid (ABA) is particularly important in some species. Treatment with only ABA induces desiccation tolerance in vegetative tissue of Borya constricta Churchill. and Craterostigma plantagineum Hochstetter. but not in the resurrection grass Sporobolus stapfianus Gandoger. Suppression of drought-induced senescence is also important for survival of drying. Further research is needed on the triggering of the induction of desiccation tolerance, on the transition between phases of protein synthesis and on the role of the phytohormone, strigolactone and other potential xylem-messengers during drying and rehydration.

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.

Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance

Resurrection plants, which are the "gifts" of natural evolution, are ideal models for studying the genetic basis of plant desiccation tolerance. Here, we report a high-quality genome assembly of 301 Mb for the diploid spike moss Selaginella tamariscina, a primitive vascular resurrection plant. We predicated 27 761 protein-coding genes from the assembled S. tamariscina genome, 11.38% (2363) of which showed significant expression changes in response to desiccation. Approximately 60.58% of the S. tamariscina genome was annotated as repetitive DNA, which is an almost 2-fold increase of that in the genome of desiccation-sensitive Selaginella moellendorffii. Genomic and transcriptomic analyses highlight the unique evolution and complex regulations of the desiccation response in S. tamariscina, including species-specific expansion of the oleosin and pentatricopeptide repeat gene families, unique genes and pathways for reactive oxygen species generation and scavenging, and enhanced abscisic acid (ABA) biosynthesis and potentially distinct regulation of ABA signaling and response. Comparative analysis of chloroplast genomes of several Selaginella species revealed a unique structural rearrangement and the complete loss of chloroplast NAD(P)H dehydrogenase (NDH) genes in S. tamariscina, suggesting a link between the absence of the NDH complex and desiccation tolerance. Taken together, our comparative genomic and transcriptomic analyses reveal common and species-specific desiccation tolerance strategies in S. tamariscina, providing significant insights into the desiccation tolerance mechanism and the evolution of resurrection plants.

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.

Perspectives on Structural, Physiological, Cellular, and Molecular Responses to Desiccation in Resurrection Plants

Resurrection plants possess a unique ability to counteract desiccation stress. Desiccation tolerance (DT) is a very complex multigenic and multifactorial process comprising a combination of physiological, morphological, cellular, genomic, transcriptomic, proteomic, and metabolic processes. Modification in the sugar composition of the hemicellulosic fraction of the cell wall is detected during dehydration. An important change is a decrease of glucose in the hemicellulosic fraction during dehydration that can reflect a modification of the xyloglucan structure. The expansins might also be involved in cell wall flexibility during drying and disrupt hydrogen bonds between polymers during rehydration of the cell wall. Cleavages by xyloglucan-modifying enzymes release the tightly bound xyloglucan-cellulose network, thus increasing cell wall flexibility required for cell wall folding upon desiccation. Changes in hydroxyproline-rich glycoproteins (HRGPs) such as arabinogalactan proteins (AGPs) are also observed during desiccation and rehydration processes. It has also been observed that significant alterations in the process of photosynthesis and photosystem (PS) II activity along with changes in the antioxidant enzyme system also increased the cell wall and membrane fluidity resulting in DT. Similarly, recent data show a major role of ABA, LEA proteins, and small regulatory RNA in regulating DT responses. Current progress in "-omic" technologies has enabled quantitative monitoring of the plethora of biological molecules in a high throughput routine, making it possible to compare their levels between desiccation-sensitive and DT species. In this review, we present a comprehensive overview of structural, physiological, cellular, molecular, and global responses involved in desiccation tolerance.

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.

Conceptualizing plant systems evolution

Organisms inhabiting extreme environments are emerging models in systems evolution, enabling us to identify the molecular alterations effecting major phenotypic divergence through comparative approaches. Here I discuss possible physiological mechanisms underlying evolutionary adaptations to extreme environments both theoretically and in relation to experimental observations. Reasoning leads me to the 'conserved steady-state' hypothesis of evolutionary adaptation: Between closely related plants adapted to differently composed soils, the homeostatically controlled steady-state set point cytosolic (buffered) concentrations of mineral ions are conserved. Subsequently, I compare molecular alterations expected to contribute to physiological adaptations with our present knowledge. Key roles of enhanced gene product dosage in plant evolutionary adaptations question the widespread stimulus response-centric paradigm. As a broader implication, co-regulation networks can lack decisive functional network elements. With this article, I hope to stimulate a discussion across research fields and provide an initial conceptual framework for future experimental testing and for quantitative modelling.

Glycerolipid analysis during desiccation and recovery of the resurrection plant Xerophyta humilis (Bak) Dur and Schinz

Xerophyta humilis is a poikilochlorophyllous monocot resurrection plant used as a model to study vegetative desiccation tolerance. Dehydration imposes tension and ultimate loss of integrity of membranes in desiccation sensitive species. We investigated the predominant molecular species of glycerolipids present in root and leaf tissues, using multiple reaction monitoring mass spectrometry, and then analysed changes therein during dehydration and subsequent rehydration of whole plants. The presence of fatty acids with long carbon chains and with odd numbers of carbons were detected and confirmed by gas chromatography. Dehydration of both leaves and roots resulted in an increase in species containing polyunsaturated fatty acids and a decrease in disaturated species. Upon rehydration, lipid saturation was reversed, with this being initiated immediately upon watering in roots but only 12-24 hr later in leaves. Relative levels of species with short-chained odd-numbered saturated fatty acids decreased during dehydration and increased during rehydration, whereas the reverse trend was observed for long-chained fatty acids. X. humilis has a unique lipid composition, this report being one of the few to demonstrate the presence of odd-numbered fatty acids in plant phosphoglycerolipids.

Heat and Drought Stresses in Crops and Approaches for Their Mitigation

Drought and heat are major abiotic stresses that reduce crop productivity and weaken global food security, especially given the current and growing impacts of climate change and increases in the occurrence and severity of both stress factors. Plants have developed dynamic responses at the morphological, physiological and biochemical levels allowing them to escape and/or adapt to unfavorable environmental conditions. Nevertheless, even the mildest heat and drought stress negatively affects crop yield. Further, several independent studies have shown that increased temperature and drought can reduce crop yields by as much as 50%. Response to stress is complex and involves several factors including signaling, transcription factors, hormones, and secondary metabolites. The reproductive phase of development, leading to the grain production is shown to be more sensitive to heat stress in several crops. Advances coming from biotechnology including progress in genomics and information technology may mitigate the detrimental effects of heat and drought through the use of agronomic management practices and the development of crop varieties with increased productivity under stress. This review presents recent progress in key areas relevant to plant drought and heat tolerance. Furthermore, an overview and implications of physiological, biochemical and genetic aspects in the context of heat and drought are presented. Potential strategies to improve crop productivity are discussed.

Heat and Drought Stresses in Crops and Approaches for Their Mitigation

Drought and heat are major abiotic stresses that reduce crop productivity and weaken global food security, especially given the current and growing impacts of climate change and increases in the occurrence and severity of both stress factors. Plants have developed dynamic responses at the morphological, physiological and biochemical levels allowing them to escape and/or adapt to unfavorable environmental conditions. Nevertheless, even the mildest heat and drought stress negatively affects crop yield. Further, several independent studies have shown that increased temperature and drought can reduce crop yields by as much as 50%. Response to stress is complex and involves several factors including signaling, transcription factors, hormones, and secondary metabolites. The reproductive phase of development, leading to the grain production is shown to be more sensitive to heat stress in several crops. Advances coming from biotechnology including progress in genomics and information technology may mitigate the detrimental effects of heat and drought through the use of agronomic management practices and the development of crop varieties with increased productivity under stress. This review presents recent progress in key areas relevant to plant drought and heat tolerance. Furthermore, an overview and implications of physiological, biochemical and genetic aspects in the context of heat and drought are presented. Potential strategies to improve crop productivity are discussed.

Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla

Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. Here we report the small 109 Mb genome of Selaginella lepidophylla, a clubmoss with extreme desiccation tolerance. Single-molecule sequencing enables accurate haplotype assembly of a single heterozygous S. lepidophylla plant, revealing extensive structural variation. We observe numerous haplotype-specific deletions consisting of largely repetitive and heavily methylated sequences, with enrichment in young Gypsy LTR retrotransposons. Such elements are active but rapidly deleted, suggesting "bloat and purge" to maintain a small genome size. Unlike all other land plant lineages, Selaginella has no evidence of a whole-genome duplication event in its evolutionary history, but instead shows unique tandem gene duplication patterns reflecting adaptation to extreme drying. Gene expression changes during desiccation in S. lepidophylla mirror patterns observed across angiosperm resurrection plants.

Current Strategies of Polyploid Plant Genome Sequence Assembly

Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.

A functional imaging study of germinating oilseed rape seed

Germination, the process whereby a dry, quiescent seed springs to life, has been a focus of plant biologist for many years, yet the early events following water uptake, during which metabolism of the embryo is restarted, remain enigmatic. Here, the nature of the cues required for this restarting in oilseed rape (Brassica napus) seed has been investigated. A holistic in vivo approach was designed to display the link between the entry and allocation of water, metabolic events and structural changes occurring during germination. For this, we combined functional magnetic resonance imaging with Fourier transform infrared microscopy, fluorescence-based respiration mapping, computer-aided seed modeling and biochemical tools. We uncovered an endospermal lipid gap, which channels water to the radicle tip, from whence it is distributed via embryonic vasculature toward cotyledon tissues. The resumption of respiration is initiated first in the endosperm, only later spreading to the embryo. Sugar metabolism and lipid utilization are linked to the spatiotemporal sequence of tissue rehydration. Together, this imaging study provides insights into the spatial aspects of key events in oilseed rape seeds leading to germination. It demonstrates how seed architecture predetermines the pattern of water intake, which sets the stage for the orchestrated restart of life.

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.