Genomes and Transcriptomes of Duckweeds

Duckweeds as edible vaccines in the animal farming industry

Animal diseases are among the most debilitating issues in the animal farming industry, resulting in decreased productivity and product quality worldwide. An emerging alternative to conventional injectable vaccines is edible vaccines, which promise increased delivery efficiency while maintaining vaccine effectiveness. One of the most promising platforms for edible vaccines is duckweeds, due to their high growth rate, ease of transformation, and excellent nutritional content. This review explores the potential, feasibility, and advantages of using duckweeds as platforms for edible vaccines. Duckweeds have proven to be superb feed sources, as evidenced by numerous improvements in both quantity (e.g., weight gain) and quality (e.g., yolk pigmentation). In terms of heterologous protein production, duckweeds, being plants, are capable of expressing proteins with complex structures and post-translational modifications. Research efforts have focused on the development of duckweed-based edible vaccines, including those against avian influenza, tuberculosis, Newcastle disease, and mastitis, among others. As with any emerging technology, the development of duckweeds as a platform for edible vaccines is still in its early stages compared to well-established injectable vaccines. It is evident that more proof-of-concept studies are required to bring edible vaccines closer to the current standards of conventional vaccines. Specifically, the duckweed expression system needs further development in areas such as yield and growth rate, especially when compared to bacterial and mammalian expression systems. Continued efforts in this field could lead to breakthroughs that significantly improve the resilience of the animal farming industry against disease threats.

Plant developmental oddities

MAIN CONCLUSION

Plants lacking shoot apical meristem develop with unique body shapes, suggesting rewiring of developmental genes. This loss of the meristem is likely influenced by a combination of environmental factors and evolutionary pressures. This study explores the development of plant bodies in three families (Podostemaceae, Lemnaceae, and Gesneriaceae) where the shoot apical meristem (SAM), a key structure for growth, is absent or altered. The review highlights alternative developmental strategies these plants employ. Also, we considered alternative reproduction in those species, namely through structures like turions, fronds, or modified leaves, bypassing the need for a SAM. Further, we report on studies based on the expression patterns of genes known to be involved in SAM formation and function. Interestingly, these genes are still present but expressed in atypical locations, suggesting a rewiring of developmental networks. Our view on the current literature and knowledge indicates that the loss or reduction of the SAM is driven by a combination of environmental pressures and evolutionary constraints, leading to these unique morphologies. Further research, also building on Next-Generation Sequencing, will be instrumental to explore the genetic basis for these adaptations and how environmental factors influence them.

Duckweed: Beyond an Efficient Plant Model System

Duckweed (Lemnaceae) rises as a crucial model system due to its unique characteristics and wide-ranging utility. The significance of physiological research and phytoremediation highlights the intricate potential of duckweed in the current era of plant biology. Special attention to duckweed has been brought due to its distinctive features of nutrient uptake, ion transport dynamics, detoxification, intricate signaling, and stress tolerance. In addition, duckweed can alleviate environmental pollutants and enhance sustainability by participating in bioremediation processes and wastewater treatment. Furthermore, insights into the genomic complexity of Lemnaceae species and the flourishing field of transgenic development highlight the opportunities for genetic manipulation and biotechnological innovations. Novel methods for the germplasm conservation of duckweed can be adopted to preserve genetic diversity for future research endeavors and breeding programs. This review centers around prospects in duckweed research promoting interdisciplinary collaborations and technological advancements to drive its full potential as a model organism.

The evolution of the duckweed ionome mirrors losses in structural complexity

BACKGROUND AND AIMS

The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of ≤14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental changes in body plan. We expect that progressive vestigiality and eventual loss of roots might have both adaptive and maladaptive consequences that are hitherto unknown.

METHODS

We quantified the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 Myr in this rapidly cycling plant (doubling times are as rapid as ~24 h). We related both micro- and macroevolutionary ionome contrasts to body plan remodelling and showed nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions.

KEY RESULTS

We observed a robust directional trend in calcium and magnesium levels, decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identified abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine (as opposed to broad) scale.

CONCLUSIONS

These data underscore the impact of root loss and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they might point to trade-offs not well recognized in ionomes.

Mechanisms of Spirodela polyrhiza tolerance to FGD wastewater-induced heavy-metal stress: Lipidomics, transcriptomics, and functional validation

Unlike terrestrial angiosperm plants, the freshwater aquatic angiosperm duckweed (Spirodela polyrhiza) grows directly in water and has distinct responses to heavy-metal stress. Plantlets accumulate metabolites, including lipids and carbohydrates, under heavy-metal stress, but how they balance metabolite levels is unclear, and the gene networks that mediate heavy-metal stress responses remain unknown. Here, we show that heavy-metal stress induced by flue gas desulfurization (FGD) wastewater reduces chlorophyll contents, inhibits growth, reduces membrane lipid biosynthesis, and stimulates membrane lipid degradation in S. polyrhiza, leading to triacylglycerol and carbohydrate accumulation. In FGD wastewater-treated plantlets, the degraded products of monogalactosyldiacylglycerol, primarily polyunsaturated fatty acids (18:3), were incorporated into triacylglycerols. Genes involved in early fatty acid biosynthesis, β-oxidation, and lipid degradation were upregulated while genes involved in cuticular wax biosynthesis were downregulated by treatment. The transcription factor gene WRINKLED3 (SpWRI3) was upregulated in FGD wastewater-treated plantlets, and its ectopic expression increased tolerance to FGD wastewater in transgenic Arabidopsis (Arabidopsis thaliana). Transgenic Arabidopsis plants showed enhanced glutathione and lower malondialdehyde contents under stress, suggesting that SpWRI3 functions in S. polyrhiza tolerance of FGD wastewater-induced heavy-metal stress. These results provide a basis for improving heavy metal-stress tolerance in plants for industrial applications.

Physiological adaptation to irradiance in duckweeds is species and accession specific and depends on light habitat niche

Duckweeds span 36 species of free-floating aquatic organisms with body sizes ranging from 2 mm to 10 mm, where each plant body plan is reduced to a largely leaf-like structure. As an emerging crop, their fast growth rates offer potential for cultivation in closed systems. We describe a novel UK collection derived from low light (dLL) or high light (dHL) habitats, profiled for growth, photosynthesis, and photoprotection (non-photochemical quenching, NPQ) responses. Twenty-three accessions of three Lemna species and one Spirodela polyrhiza were grown under relatively low light (LL: 100 μmol m-2 s-1) and high light (HL: 350 μmol m-2 s-1) intensities. We observed broad within- and between-species level variation in photosynthesis acclimation. Duckweeds grown under HL exhibited a lower growth rate, biomass, chlorophyll, and quantum yield of photosynthesis. In HL compared with LL, carotenoid de-epoxidation state and NPQ were higher, whilst PSII efficiency (φPSII) and Chl a:b ratios were unchanged. The dLL plants showed relatively stronger acclimation to HL compared with dHL plants, especially Lemna japonica accessions. These achieved faster growth in HL with concurrent higher carotenoid levels and NPQ, and less degradation of chlorophyll. We conclude that these data support local adaptation to the light environment in duckweed affecting acclimation in controlled conditions.

Heavy metals/-metalloids (As) phytoremediation with Landoltia punctata and Lemna sp. (duckweeds): coupling with biorefinery prospects for sustainable phytotechnologies

Heavy metals/-metalloids can result in serious human health hazards. Phytoremediation is green bioresource technology for the remediation of heavy metals and arsenic (As). However, there exists a knowledge gap and systematic information on duckweed-based metal phytoremediation in an eco-sustainable way. Therefore, the present review offers a critical discussion on the effective use of duckweeds (genera Landoltia and Lemna)-based phytoremediation to decontaminate metallic contaminants from wastewater. Phytoextraction and rhizofiltration were the major mechanism in 'duckweed bioreactors' that can be dependent on physico-chemical factors and plant-microbe interactions. The biotechnological advances such as gene manipulations can accelerate the duckweed-based phytoremediation process. High starch and protein contents of the metal-loaded duckweed biomass facilitate their use as feedstock in biorefinery. Biorefinery prospects such as bioenergy production, value-added products, and biofertilizers can augment the circular economy approach. Coupling duckweed-based phytoremediation with biorefinery can help achieve Sustainable Development Goals (SDGs) and human well-being.

Immunobiodiversity: Conserved and specific immunity across land plants and beyond

Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.

Differential Morpho-Physiological and Biochemical Responses of Duckweed Clones from Saudi Arabia to Salinity

Salinity affects the morphological, physiological, and biochemical characteristics of several plant species. The current study was conducted to investigate differential salt tolerance potentials among ten duckweed clones under different salt-stress conditions. Morphological and physiological parameters, including fronds length, fronds number, root length, root number, Na+/K+, chlorophyll, proline contents, and fresh harvest weight, were recorded for each of the ten duckweed clones collected from different Saudi Arabia regions. Additionally, the expression patterns of seven salt-related genes were monitored in a salt-tolerant duckweed genotype. The results show that the Madinah-2 (Spirodela polyryiza) and Al-Qassim (Landoltia punctata) clones presented higher performances for all the tested morphological and physiological parameters compared to other genotypes under salt-stress conditions. At concentrations greater than 150 mM NaCl, these aforementioned traits were affected for all the genotypes tested, except Madinah-2 (S. polyryiza) and Al-Qassim (L. punctata) clones, both of which exhibited high tolerance behavior under high salt conditions (200 mM and 250 mM NaCl). The principal component analysis (PCA) showed that the first five principal components accounted for 94.8% of the total variance among the studied traits. Morphological and physiological traits are the major portions of PC1. Moreover, the expression pattern analysis of NHX, BZIP, ST, and KTrans transcript revealed their upregulation in the Al-Qassim clone under salt-stress conditions, suggesting that these genes play a role in this clone's tolerance to salt-induced stress. Overall, this study indicates that the Al-Qassim clone could be used in a brackish-water duckweed-based treatment program with a simultaneous provision of valuable plant biomass.

Heavy metals and arsenic stress in food crops: Elucidating antioxidative defense mechanisms in hyperaccumulators for food security, agricultural sustainability, and human health

The spread of heavy metal(loid)s at soil-food crop interfaces has become a threat to sustainable agricultural productivity, food security, and human health. The eco-toxic effects of heavy metals on food crops can be manifested through reactive oxygen species that have the potential to disturb seed germination, normal growth, photosynthesis, cellular metabolism, and homeostasis. This review provides a critical overview of stress tolerance mechanisms in food crops/hyperaccumulator plants against heavy metals and arsenic (HM-As). The HM-As antioxidative stress tolerance in food crops is associated with changes in metabolomics (physico-biochemical/lipidomics) and genomics (molecular level). Furthermore, HM-As stress tolerance can occur through plant-microbe, phytohormone, antioxidant, and signal molecule interactions. Information regarding the avoidance, tolerance, and stress resilience of HM-As should help pave the way to minimize food chain contamination, eco-toxicity, and health risks. Advanced biotechnological approaches (e.g., genome modification with CRISPR-Cas9 gene editing) in concert with traditional sustainable biological methods are useful options to develop 'pollution safe designer cultivars' with increased climate change resilience and public health risks mitigation. Further, the usage of HM-As tolerant hyperaccumulator biomass in biorefineries (e.g., environmental remediation, value added chemicals, and bioenergy) is advocated to realize the synergy between biotechnological research and socio-economic policy frameworks, which are inextricably linked with environmental sustainability. The biotechnological innovations, if directed toward 'cleaner climate smart phytotechnologies' and 'HM-As stress resilient food crops', should help open the new path to achieve sustainable development goals (SDGs) and a circular bioeconomy.

Duckweeds for Phytoremediation of Polluted Water

Tiny aquatic plants from the Lemnaceae family, commonly known as duckweeds, are often regarded as detrimental to the environment because of their ability to quickly populate and cover the surfaces of bodies of water. Due to their rapid vegetative propagation, duckweeds have one of the fastest growth rates among flowering plants and can accumulate large amounts of biomass in relatively short time periods. Due to the high yield of valuable biomass and ease of harvest, duckweeds can be used as feedstock for biofuels, animal feed, and other applications. Thanks to their efficient absorption of nitrogen- and phosphate-containing pollutants, duckweeds play an important role in the restorative ecology of water reservoirs. Moreover, compared to other species, duckweed species and ecotypes demonstrate exceptionally high adaptivity to a variety of environmental factors; indeed, duckweeds remove and convert many contaminants, such as nitrogen, into plant biomass. The global distribution of duckweeds and their tolerance of ammonia, heavy metals, other pollutants, and stresses are the major factors highlighting their potential for use in purifying agricultural, municipal, and some industrial wastewater. In summary, duckweeds are a powerful tool for bioremediation that can reduce anthropogenic pollution in aquatic ecosystems and prevent water eutrophication in a simple, inexpensive ecologically friendly way. Here we review the potential for using duckweeds in phytoremediation of several major water pollutants: mineral nitrogen and phosphorus, various organic chemicals, and heavy metals.

Examination of the Metallothionein Gene Family in Greater Duckweed Spirodela polyrhiza

Duckweeds are aquatic plants that proliferate rapidly in a wide range of freshwaters, and they are regarded as a potential source of sustainable biomass for various applications and the cost-effective bioremediation of heavy metal pollutants. To understand the cellular and molecular basis that underlies the high metal tolerance and accumulation capacity of duckweeds, we examined the forms and transcript profiles of the metallothionein (MT) gene family in the model duckweed Spirodela polyrhiza, whose genome has been completely sequenced. Four S. polyrhiza MT-like genes were identified and annotated as SpMT2a, SpMT2b, SpMT3, and SpMT4. All except SpMT2b showed high sequence homology including the conserved cysteine residues with the previously described MTs from flowering plants. The S. polyrhiza genome appears to lack the root-specific Type 1 MT. The transcripts of SpMT2a, SpMT2b, and SpMT3 could be detected in the vegetative whole-plant tissues. The transcript abundance of SpMT2a was upregulated several-fold in response to cadmium stress, and the heterologous expression of SpMT2a conferred copper and cadmium tolerance to the metal-sensitive ∆cup1 strain of Saccharomyces cerevisiae. Based on these results, we proposed that SpMT2a may play an important role in the metal detoxification mechanism of duckweed.

Duckweed: a potential phytosensor for heavy metals

Globally, heavy metal (HM) contamination is one of the primary causes of environmental pollution leading to decreased quality of life for those affected. In particular, HM contamination in groundwater poses a serious risk to human health and the potential for destabilization of aquatic ecosystems. At present, strategies to remove HM contamination from wastewater are inefficient, costly, laborious, and often the removal poses as much risk to the environment as the initial contamination. Phytoremediation, plant-based removal of contaminants from soil or water, has long been viewed as an economical and sustainable solution to remove toxic metals from the environment. However, to date, phytoremediation has demonstrated limited successes despite a large volume of literature supporting its potential. A key aspect for achieving robust and meaningful phytoremediation is the selection of a plant species that is well suited to the task. For the removal of pollutants from wastewater, hydrophytes, like duckweed, exhibit significant potential due to their rapid growth on nutrient-rich water, ease of collection, and ability to survive in various ecosystems. As a model for ecotoxicity studies, duckweed is an ideal candidate, as it is easy to cultivate under controlled and even sterile conditions, and the rapid growth enables multi-generational studies. Similarly, recent advances in the genetic engineering and genome-editing of duckweed will enable the transition from fundamental ecotoxicity studies to engineered solutions for phytoremediation of HMs. This review will provide insight into the suitability of duckweeds for phytoremediation of HMs and strategies for engineering next-generation duckweed to provide real-world environmental solutions.

Automated imaging of duckweed growth and development

Duckweeds are the smallest angiosperms, possessing a simple body architecture and highest rates of biomass accumulation. They can grow near-exponentially via clonal propagation. Understanding their reproductive biology, growth, and development is essential to unlock their potential for phytoremediation, carbon capture, and nutrition. However, there is a lack of non-laborious and convenient methods for spatially and temporally imaging an array of duckweed plants and growth conditions in the same experiment. We developed an automated microscopy approach to record time-lapse images of duckweed plants growing in 12-well cell culture plates. As a proof-of-concept experiment, we grew duckweed on semi-solid media with and without sucrose and monitored its effect on their growth over 3 days. Using the PlantCV toolkit, we quantified the thallus area of individual plantlets over time, and showed that L. minor grown on sucrose had an average growth rate four times higher than without sucrose. This method will serve as a blueprint to perform automated high-throughput growth assays for studying the development patterns of duckweeds from different species, genotypes, and conditions.

Intraspecific Diversity in Aquatic Ecosystems: Comparison between Spirodela polyrhiza and Lemna minor in Natural Populations of Duckweed

Samples of two duckweed species, Spirodela polyrhiza and Lemna minor, were collected around small ponds and investigated concerning the question of whether natural populations of duckweeds constitute a single clone, or whether clonal diversity exists. Amplified fragment length polymorphism was used as a molecular method to distinguish clones of the same species. Possible intraspecific diversity was evaluated by average-linkage clustering. The main criterion to distinguish one clone from another was the 95% significance level of the Jaccard dissimilarity index for replicated samples. Within natural populations of L. minor, significant intraspecific genetic differences were detected. In each of the three small ponds harbouring populations of L. minor, based on twelve samples, between four and nine distinct clones were detected. Natural populations of L. minor consist of a mixture of several clones representing intraspecific biodiversity in an aquatic ecosystem. Moreover, identical distinct clones were discovered in more than one pond, located at a distance of 1 km and 2.4 km from each other. Evidently, fronds of L. minor were transported between these different ponds. The genetic differences for S. polyrhiza, however, were below the error-threshold of the method within a pond to detect distinct clones, but were pronounced between samples of two different ponds.

Characterization of Various Subunit Combinations of ADP-Glucose Pyrophosphorylase in Duckweed (Landoltia punctata)

Background

Landoltia punctata can be used as renewable and sustainable biofuel feedstock because it can quickly accumulate high starch levels. ADP-glucose pyrophosphorylase (AGPase) catalyzes the first committed step during starch biosynthesis in higher plants. The heterotetrameric structure of plant AGPases comprises pairs of large subunits (LSs) and small subunits (SSs). Although several studies have reported on the high starch accumulation capacity of duckweed, no study has explored the underlying molecular accumulation mechanisms and their linkage with AGPase. Therefore, this study focused on characterizing the roles of different L. punctate AGPases. Methodology. Expression patterns of LpAGPs were determined through comparative transcriptome analyses, followed by coexpressing their coding sequences in Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Nicotiana tabacum.

Results

Comparative transcriptome analyses showed that there are five AGPase subunits encoding cDNAs in L. punctata (LpAGPS1, LpAGPS2, LpAGPL1, LpAGPL2, and LpAGPL3). Nutrient starvation (distilled water treatment) significantly upregulated the expression of LpAGPS1, LpAGPL2, and LpAGPL3. Coexpression of LpAGPSs and LpAGPLs in Escherichia coli generated six heterotetramers, but only four (LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3) exhibited AGPase activities and displayed a brownish coloration upon exposure to iodine staining. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays validated the interactions between LpAGPS1/LpAGPL2, LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3. All the five LpAGPs were fusion-expressed with hGFP in Arabidopsis protoplasts, and their green fluorescence signals were uniformly localized in the chloroplast, indicating that they are plastid proteins.

Conclusions

This study uncovered the cDNA sequences, structures, subunit interactions, expression patterns, and subcellular localization of AGPase. Collectively, these findings provide new insights into the molecular mechanism of fast starch accumulation in L. punctata.

Riddled with holes: Understanding air space formation in plant leaves

Plants use energy from sunlight to transform carbon dioxide from the air into complex organic molecules, ultimately producing much of the food we eat. To make this complex chemistry more efficient, plant leaves are intricately constructed in 3 dimensions: They are flat to maximise light capture and contain extensive internal air spaces to increase gas exchange for photosynthesis. Many years of work has built up an understanding of how leaves form flat blades, but the molecular mechanisms that control air space formation are poorly understood. Here, I review our current understanding of air space formation and outline how recent advances can be harnessed to answer key questions and take the field forward. Increasing our understanding of plant air spaces will not only allow us to understand a fundamental aspect of plant development, but also unlock the potential to engineer the internal structure of crops to make them more efficient at photosynthesis with lower water requirements and more resilient in the face of a changing environment.

Leaves are interwoven with large air spaces to increase the efficiency of photosynthesis; however, how these air spaces form and how different patterns have evolved is almost unknown. This Unsolved Mystery article discusses the existing evidence and poses new avenues of research to answer this question.

Lemnaceae and Orontiaceae Are Phylogenetically and Morphologically Distinct from Araceae

Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence has called into question their phylogenetic independence, with some authors asserting instead that duckweeds should be reclassified as subfamily Lemnoideae of an expanded family Araceae. Although a close phylogenetic relationship of duckweeds with traditional Araceae has been supported by multiple studies, the taxonomic disposition of duckweeds must be evaluated more critically to promote nomenclatural stability and utility. Subsuming duckweeds as a morphologically incongruent lineage of Araceae effectively eliminates the family category of Lemnaceae that has been widely used for many years. Instead, we suggest that Araceae subfamily Orontioideae should be restored to family status as Orontiaceae, which thereby would enable the recognition of three morphologically and phylogenetically distinct lineages: Araceae, Lemnaceae, and Orontiaceae.

Morphological Characterization and DNA Barcoding of Duckweed Species in Saudi Arabia

Duckweeds, or Lemnaceae, are widespread aquatic plants. Morphology-based identification of duckweed species is difficult because of their structural complexity. Hence, molecular tools provide significant advantages for characterizing and selecting species or clones for sustainable commercial use. In this study, we collected and characterized ten duckweed isolates from nine different regions in Saudi Arabia (SA). Based on the morphological characterization and phylogenetic analysis of intergenic spacer sequences of chloroplast DNA using six barcoding markers, the clones were classified into three genera, represented by seven species: Lemna gibba L., Lemna minor L., Lemna japonica Landolt, Lemna aequinoctialis Welw., Lemna perpusilla Torr., Spirodela polyryiza (L.) Schleid., and Landoltia punctate G. Mey. Lemna gibba was revealed to be a distinct dominant duckweed species in many regions of SA. Five barcoding markers showed that L. gibba, L. minor, and L. punctata were the most widely distributed species in the country. However, L. punctata, L. perpusilla, and S. polyryiza were the dominant species in the Al-Qassim, Madinah-1, and Madinah-2 regions, respectively. Moreover, the morphological traits revealed variations for these clones, relative to other studied duckweed clones. According to the results obtained in this study, three out of six plastid markers (trnH-psbA, matK, and atpF-atpH) helped to identify the dominant duckweed species in Saudi Arabia. Further evaluation based on adaptability, molecular genetic studies, and functional genomics is needed for these species to be used at the commercial level in Saudi Arabia.

Genomic analysis of the polyamine biosynthesis pathway in duckweed Spirodela polyrhiza L.: presence of the arginine decarboxylase pathway, absence of the ornithine decarboxylase pathway, and response to abiotic stresses

Identification of the polyamine biosynthetic pathway genes in duckweed S. polyrhiza reveals presence of prokaryotic as well as land plant-type ADC pathway but absence of ODC encoding genes. Their differential gene expression and transcript abundance is shown modulated by exogenous methyl jasmonate, salinity, and acidic pH. Genetic components encoding for polyamine (PA) biosynthetic pathway are known in several land plant species; however, little is known about them in aquatic plants. We utilized recently sequenced three duckweed (Spirodela polyrhiza) genome assemblies to map PA biosynthetic pathway genes in S. polyrhiza. PA biosynthesis in most higher plants except for Arabidopsis involves two pathways, via arginine decarboxylase (ADC) and ornithine decarboxylase (ODC). ADC-mediated PA biosynthetic pathway genes, namely, one arginase (SpARG1), two arginine decarboxylases (SpADC1, SpADC2), one agmatine iminohydrolase/deiminase (SpAIH), one N-carbamoyl putrescine amidase (SpCPA), three S-adenosylmethionine decarboxylases (SpSAMDc1, 2, 3), one spermidine synthase (SpSPDS1) and one spermine synthase (SpSPMS1) in S. polyrhiza genome were identified here. However, no locus was found for ODC pathway genes in this duckweed. Hidden Markov Model protein domain analysis established that SpADC1 is a prokaryotic/biodegradative type ADC and its molecular phylogenic classification fell in a separate prokaryotic origin ADC clade with SpADC2 as a biosynthetic type of arginine decarboxylase. However, thermospermine synthase (t-SPMS)/Aculis5 genes were not found present. Instead, one of the annotated SPDS may also function as SPMS, since it was found associated with the SPMS phylogenetic clade along with known SPMS genes. Moreover, we demonstrate that S. polyrhiza PA biosynthetic gene transcripts are differentially expressed in response to unfavorable conditions, such as exogenously added salt, methyl jasmonate, or acidic pH environment as well as in extreme temperature regimes. Thus, S. polyrhiza genome encodes for complete polyamine biosynthesis pathway and the genes are transcriptionally active in response to changing environmental conditions suggesting an important role of polyamines in this aquatic plant.

Research Progress of a Potential Bioreactor: Duckweed

Recently, plant bioreactors have flourished into an exciting area of synthetic biology because of their product safety, inexpensive production cost, and easy scale-up. Duckweed is the smallest and fastest-growing aquatic plant, and has advantages including simple processing and the ability to grow high biomass in smaller areas. Therefore, duckweed could be used as a new potential bioreactor for biological products such as vaccines, antibodies, pharmaceutical proteins, and industrial enzymes. Duckweed has made a breakthrough in biosynthesis as a chassis plant and is being utilized for the production of plenty of biological products or bio-derivatives with multiple uses and high values. This review summarizes the latest progress on genetic background, genetic transformation system, and bioreactor development of duckweed, and provides insights for further exploration and application of duckweed.

Identification, Phylogeny, and Comparative Expression of the Lipoxygenase Gene Family of the Aquatic Duckweed, Spirodela polyrhiza, during Growth and in Response to Methyl Jasmonate and Salt

Lipoxygenases (LOXs) (EC 1.13.11.12) catalyze the oxygenation of fatty acids and produce oxylipins, including the plant hormone jasmonic acid (JA) and its methyl ester, methyl jasmonate (MeJA). Little information is available about the LOX gene family in aquatic plants. We identified a novel LOX gene family comprising nine LOX genes in the aquatic plant Spirodela polyrhiza (greater duckweed). The reduced anatomy of S. polyrhiza did not lead to a reduction in LOX family genes. The 13-LOX subfamily, with seven genes, predominates, while the 9-LOX subfamily is reduced to two genes, an opposite trend from known LOX families of other plant species. As the 13-LOX subfamily is associated with the synthesis of JA/MeJA, its predominance in the Spirodela genome raises the possibility of a higher requirement for the hormone in the aquatic plant. JA-/MeJA-based feedback regulation during culture aging as well as the induction of LOX gene family members within 6 h of salt exposure are demonstrated.

Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed

Background

Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown.

Results

In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interactions in the regulation of salt stress responses. Finally, a representative network of lncRNA-miRNA-mRNA was proposed and discussed to participate in duckweed salt stress via auxin signaling.

Conclusions

This study is the first report on salt-responsive lncRNAs in duckweed, and the findings will provide a solid foundation for in-depth functional characterization of duckweed lncRNAs in response to salt stress.

Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes

Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, ~ 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) > 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri- (14.9%), tetra- (4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM ≤ 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.

Declined cadmium accumulation in Na+/H+ antiporter (NHX1) transgenic duckweed under cadmium stress

Cadmium (Cd) is a serious threat to plants health. Though some genes have been reported to get involved in the regulation of tolerance to Cd, the mechanisms underlying this process are not fully understood. Na⁺/H⁺ antiporter (NHX1) plays an important role in Na⁺/H⁺ trafficking. The salt and cadmium stress tolerance were found to be enhanced by NHX1 in duckweed according to our previous study, however, its function in Cd²⁺ flux under Cd stress has not been studied. Here we explored the Cd²⁺ flux in wild type (WT) and NHX1 transgenic duckweed (NHX1) under Cd stress. We found that the Cd²⁺ influx in NHX1 duckweed was significantly declined, followed by an increased Cd²⁺ efflux after 20 min treatment of Cd, which resulted a less accumulation of Cd in NHX1. Reversely, inhibition of NHX1 by amiloride treatment, enhanced Cd²⁺ influx in NHX1 duckweed, subsequently delayed Cd²⁺ efflux in both genotypes of duckweed under Cd²⁺ shock. H⁺ efflux in NHX1 duckweed was lower compare with that in WT with 20 min Cd²⁺ shock. NHX1 also increased the pH value with Cd²⁺ stress in the transgenic rhizoid. These finding suggested a new function of NHX1 in regulation of Cd²⁺ and H⁺ flow during short-term Cd²⁺ shock.

Physiological and Transcriptomic Analysis Reveals Distorted Ion Homeostasis and Responses in the Freshwater Plant Spirodela polyrhiza L. under Salt Stress

Duckweeds are a family of freshwater angiosperms with morphology reduced to fronds and propagation by vegetative budding. Unlike other angiosperm plants such as Arabidopsis and rice that have physical barriers between their photosynthetic organs and soils, the photosynthetic organs of duckweeds face directly to their nutrient suppliers (waters), therefore, their responses to salinity may be distinct. In this research, we found that the duckweed Spirodela polyrhiza L. accumulated high content of sodium and reduced potassium and calcium contents in large amounts under salt stress. Fresh weight, Rubisco and AGPase activities, and starch content were significantly decreaseded in the first day but recovered gradually in the following days and accumulated more starch than control from Day 3 to Day 5 when treated with 100 mM and 150 mM NaCl. A total of 2156 differentially expressed genes were identified. Overall, the genes related to ethylene metabolism, major CHO degradation, lipid degradation, N-metabolism, secondary metabolism of flavonoids, and abiotic stress were significantly increased, while those involved in cell cycle and organization, cell wall, mitochondrial electron transport of ATP synthesis, light reaction of photosynthesis, auxin metabolism, and tetrapyrrole synthesis were greatly inhibited. Moreover, salt stress also significantly influenced the expression of transcription factors that are mainly involved in abiotic stress and cell differentiation. However, most of the osmosensing calcium antiporters (OSCA) and the potassium inward channels were downregulated, Na⁺/H⁺ antiporters (SOS1 and NHX) and a Na⁺/Ca²⁺ exchanger were slightly upregulated, but most of them did not respond significantly to salt stress. These results indicated that the ion homeostasis was strongly disturbed. Finally, the shared and distinct regulatory networks of salt stress responses between duckweeds and other plants were intensively discussed. Taken together, these findings provide novel insights into the underlying mechanisms of salt stress response in duckweeds, and can be served as a useful foundation for salt tolerance improvement of duckweeds for the application in salinity conditions.