Biotic Defense Research Articles

TNFα has differential effects on the transcriptome profile of selected populations in murine cartilage

ObjectiveTo further our understanding of the role of tumor necrosis factor (TNF)α on the inflammatory response in chondrocytes. DesignWe explored the effects of TNFα on the transcriptome of epiphyseal chondrocytes from newborn C57BL/6 mice at the total and single cell (sc) resolution. ResultsGene set enrichment analysis of total RNA-Seq from TNFα-treated chondrocytes revealed enhanced response to biotic stimulus, defense and immune response and cytokine signaling and suppressed cartilage and skeletal morphogenesis and development. scRNA-Seq analyzed 14,239 ​cells and 24,320 genes and distinguished 16 ​cell clusters. The more prevalent ones were constituted by limb bud and chondrogenic cells and fibroblasts comprising ∼73 ​% of the cell population. Genes expressed by joint fibroblasts were detected in 5 clusters comprising ∼45 ​% of the cells isolated. Pseudotime trajectory finding revealed an association between fibroblast and chondrogenic clusters which was not modified by TNFα. TNFα decreased the total cells recovered by 18.5 ​% and the chondrogenic, limb bud and mesenchymal clusters by 32 ​%, 27 ​% and 7 ​%, respectively. TNFα had profound effects on the insulin-like growth factor (IGF) axis decreasing Igf1, Igf2 and Igfbp4 and inducing Igfbp3 and Igfbp5, explaining an inhibition of collagen biosynthesis, cartilage and skeletal morphogenesis. Ingenuity Pathway Analysis of scRNA-Seq data revealed that TNFα enhanced the osteoarthritis, rheumatoid arthritis, pathogen induced cytokine storm and interleukin 6 signaling pathways and suppressed fibroblast growth factor signaling. ConclusionsEpiphyseal chondrocytes are constituted by diverse cell populations distinctly regulated by TNFα to promote inflammation and suppression of matrix biosynthesis and growth.

Integrated genome-wide association and transcriptomic studies reveal genetic architecture of bulb storability of plentiful garlic germplasm resources

Abstract Garlic is a widely utilized condiments and health product. However, garlic bulbs are prone to quality deterioration resulting in decrease of economic value during postharvest. In this study, the storability of 501 garlic accessions worldwide was evaluated based on the examination of decay index (DI), decay rate, sprouting rate, and bud to clove ratio in two consecutive years. The DI was employed as a primary index for evaluating the storability of garlic. Among these garlic, 43 accessions exhibited strong storability with DI of 0-5%. Phenotypic and cytological observations revealed that strong-storability accessions displayed delayed sprouting and decay, a slow rate of nutrient transfer to vascular bundles. Through genome-wide association study (GWAS), 234 single nucleotide polymorphism loci (SNPs) were associated with the storability, which were located in or near 401 genes, which were annotated the functions of resistance, storage substances transport, etc. Total of 44 genes were screened using selective sweep analysis. Transcriptomic analysis was performed at four periods after storage in the 8N035 accession with strong-storability and 8N258 accession with weak-storability. Differentially expressed genes (DEGs) were up-regulated in the 8N258 compared with 8N035 were enriched in photosynthesis and stress response, whereas the down-regulated genes were enriched in response of biotic and abiotic stress and defense response. A co-expression network and GWAS identified three hub genes as key regulatory genes. Conjoint analysis of GWAS, selective sweep and transcriptomic analysis identified 21 important candidate genes. These findings provided excellent resources with storability and vital candidate genes regulating storability for biological breeding of garlic.

Unveiling the genetic landscape: Exploring the SSR-based genetic architecture and amino acid dissection of Gossypium barbadense and G. darwinii genomes

Genetic maps highlight the genome organization and structure but also provide the chance of tagging superior traits for crop improvement through marker-assisted selection. Amino acids are building blocks of proteins and perform crucial function in regulating the signaling of molecules involved in the development and growth of plants. Plant architecture also have an impact on crop productivity. In order to select elite cultivars for breeding and identification of favorable alleles and their functional properties, a deep understanding of genetic architecture and development of genetic map is essential. In present investigation, an interspecific cross of Gossypium barbadense XH-18 × G. darwinii 5-7 was made to develop a genetic map utilizing single sequence repeat markers for the dissection of amino acids involved in genetic architecture of G. barbadense and G. darwinii. We measured chromosomal distribution of 20 amino acids across the whole genome of both species. The map consists of 613 markers spread across all 26 chromosomes, covering 2371.4 cM of cotton genome with an average inter-marker distance of 9.35 cM. The marker number anchored on the chromosomes varied from 5 to 76 with an average of 23.57 on each chromosome. The Dt sub-genome had more markers (83.03%) than the At sub-genome (15.66%). Moreover, the longest chromosome was 143.387 cM, the shortest was 58.430 cM, and the average length was 91.207 cM. The Dt subgenome spans a greater genomic distance than the At subgenome. A sum of 21,035 genes were discovered, covering the complete genome of G. barbadense; G. darwinii and have been found to be involved in tRNA 3'-trailer cleavage, macromolecule modification, peptide deformylase activity, response to biotic stimulus and defense response. The minimum Glutamic acid (Glu), Histidine (His), and Lysine (Lys) were found on Chr.13 (0.00-17.74), Chr.02 (0.00-8.01), and Chr.06 (0.00-17.97), respectively found through chromosomal amino acid dissection. The genome-wide SSR interspecific genetic map of G. barbadense and G. darwinii is first of its kind, and studying chromosomal distribution of amino acids will set a landmark step to dissect the genome structure of G. darwinii.

In vitro evaluation of antiviral activity in carnivorous plant species

Sarracenia purpurea is a carnivorous plant historically used to treat smallpox infections. Our previous data found S. purpurea had broad spectrum antiviral activity in vitro. S. purpurea is one of several hundred identified carnivorous species of plants. Carnivorous plants have evolved through convergent evolution in at least ten independent events, usually in response to harsh environments where nutrition from prey is required for growth. These prey are known vectors of plant viruses that might introduce novel biotic stressors and defense pathways in carnivorous plants. This study evaluated the antiviral activity of several non-carnivorous and carnivorous plants from four evolutionarily distinct clades. Results demonstrated that carnivorous plants have evolved antiviral activity, a trait that is not present in related species of non-carnivorous plants. The antiviral trait may be due to the plant-prey relationship with insect vectors and an evolutionary need for carnivorous plants to have more robust antiviral defense systems.

Morphological divergence of domatia in ant-free populations of the widespread Neotropical myrmecophyte Miconia tococa (Melastomataceae)

Abstract Co-evolving organisms experience multiple selection pressures that may lead to trait mismatches among different populations and sites. In defensive ant–plant mutualisms, host plants (myrmecophytes) produce specialized shelters (domatia) to harbour specialized ant-partners in exchange for protection against enemies. Although populations of myrmecophytes without ants occur in some locations, there are no records of changes in domatia morphology—at the population level—due to the absence of symbiotic ants. We conducted broad-scale samplings of Miconia tococa (Melastomataceae) populations across the Brazilian Cerrado and a 2-year transplant experiment to test whether domatia morphology changes when symbiotic ants are naturally absent. Domatia were 33.9% smaller in ant-free populations than in ant-inhabited populations. Transplants revealed that host plants from ant-inhabited sites still developed larger domatia than those from ant-free sites, even in the absence of ant-partners. These findings point to a change of M. tococa traits associated with biotic defences where symbiotic ants are absent. What may have begun as a plastic adjustment to ant-free environments appears to have been transformed into fixed (genetic) interpopulation differences over time, indicating a potential local destabilization of the mutualism or a mechanism to stabilize the interaction at the landscape scale.

The Dynamic Interaction between Oil Palm and Phytophthora palmivora in Bud Rot Disease: Insights from Transcriptomic Analysis and Network Modelling.

Bud Rot, caused by Phytophthora palmivora, is considered one of the main diseases affecting African oil palm (Elaeis guineensis). In this study, we investigated the in vitro molecular dynamics of the pathogen-host interaction by analyzing gene expression profiles from oil palm genotypes that were either susceptible or resistant to the disease. We observed distinct interactions of P. palmivora with resistant and susceptible oil palms through co-expression network analysis. When interacting with susceptible genotypes, P. palmivora exhibited upregulation of carbohydrate and sulfate transport genes. These genes demonstrated co-expression with apoplastic and cytoplasmic effectors, including cell wall degrading enzymes, elicitins, and RxLR motif effectors. The pathogen manipulated susceptible oil palm materials, exacerbating the response and compromising the phenylpropanoid pathway, ultimately leading to susceptibility. In contrast, resistant materials exhibited control over their response through putative Heat Shock Proteins (HSP) that maintained homeostasis between primary metabolism and biotic defense. Co-expressed genes related to flavonoids, WRKY transcripts, lectin-type receptors, and LRR receptors may play important roles in pathogen control. Overall, the study provides new knowledge of the molecular mechanisms underlying the interaction between E. guineensis and P. palmivora, which can contribute to controlling Bud Rot in oil palms and gives new insights into the interactions of P. palmivora with their hosts.

Physiological, molecular, and genetic mechanism of action of the biostimulant Quantis™ for increased thermotolerance of potato (Solanum tuberosum L.)

BackgroundRaising global temperatures limit crop productivity and new strategies are needed to improve the resilience of thermosensitive crops such as potato (Solanum tuberosum L.). Biostimulants are emerging as potential crop protection products against environmental stress, however their mechanism of action remains largely unknown, hindering their wider adoption. We used comprehensive physiological, molecular, and mass spectrometry approaches to develop understanding of the mechanism of plant thermotolerance exerted by the biostimulant, Quantis™, under heat stress. Using orthologues gene mutations in Arabidopsis thaliana we report heat-defence genes, modified by Quantis™, which were also investigated for potential overlapping functions in biotic stress defence to Sclerotinia sclerotiorum and Rhizoctonia solani.ResultsQuantis™ enhanced PSII photochemical efficiency and decreased thermal dissipation of potato grown under heat stress. These effects were associated with upregulation of genes with antioxidant function, including PR10, flavonoid 3′‐hydroxylase and β-glucosidases, and modulation of abscisic acid (ABA) and cytokinin (CK) activity in leaves by Quantis™. The biostimulant modulated the expression of the heat-defence genes, PEN1, PR4 or MEE59, with functions in leaf photoprotection and root thermal protection, but with no overlapping function in biotic stress defence. Protective root growth under heat stress, following the biostimulant application, was correlated with enhanced CK signalling in roots. Increased endogenous concentrations of ABA and CK in potato leaves and significant upregulation of StFKF1 were consistent with tuberisation promoting effects. Quantis™ application resulted in 4% tuber weight increase and 40% larger tuber size thus mitigating negative effects of heat stress on tuber growth.ConclusionsQuantis™ application prior to heat stress effectively primed heat tolerance responses and alleviated temperature stress of S. tuberosum L. and A. thaliana by modulating the expression and function of PR4 and MEE59 and by regulating CK activity above and below ground, indicating that the mechanism of action of the biostimulant is conserved, and will be effective in many plant species. Thus, a biostimulant application targeting the most susceptible crop developmental stages to heat disorders can be effectively integrated within future agronomy practices to mitigate losses in other thermosensitive crops.Graphical

Plant physiology: The overturning of assumed functional relevance of ‘salt’ bladders

For decades, the function of epidermal bladder cells in quinoa and iceplant was thought to be physiological because of their function in a related species. Exciting new research carefully demolishes that assumption, suggesting that these structures serve primarily biotic defense roles, setting up a great many interesting, important questions.

Retinal transcriptome profiling identifies novel candidate genes associated with visual impairment in a mouse model of multiple sclerosis

ABSTRACT Visual impairment is occasionally observed in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE). Although uveitis and optic neuritis have been reported in MS and EAE, the precise mechanisms underlying the pathogenesis of these visual impairments remain poorly understood. This study aims to identify differentially expressed genes (DEGs) in the retinas of mice with EAE to identify genes that may be implicated in EAE-induced visual impairment. Fourteen adult mice were injected with myelin oligodendrocyte glycoprotein35–55 to induce the EAE model. Transcriptomes of retinas with EAE were analyzed by RNA-sequencing. Gene expression analysis revealed 347 DEGs in the retinas of mice with EAE: 345 were upregulated, and 2 were downregulated (adjusted p-value < 0.05 and absolute log2 fold change > 1). Gene ontology (GO) analysis showed that the upregulated genes in the retinas of mice with EAE were primarily related to immune responses, responses to external biotic stimuli, defense responses, and leukocyte-mediated immunity in the GO biological process. The expression of six upregulated hub genes (c1qb, ctss, itgam, itgb2, syk, and tyrobp) from the STRING analysis and the two significantly downregulated DEGs (hapln1 and ndst4) were validated by reverse transcription-quantitative polymerase chain reaction. In addition, gene set enrichment analysis showed that the negatively enriched gene sets in EAE-affected retinas were associated with the neuronal system and phototransduction cascade. This study provides novel molecular evidence for visual impairments in EAE and indicates directions for further research to elucidate the mechanisms of these visual impairments in MS.

Photosynthetic and transcriptome responses to fluctuating light in Arabidopsis thylakoid ion transport triple mutant.

Fluctuating light intensity challenges fluent photosynthetic electron transport in plants, inducing photoprotection while diminishing carbon assimilation and growth, and also influencing photosynthetic signaling for regulation of gene expression. Here, we employed in vivo chlorophyll-a fluorescence and P700 difference absorption measurements to demonstrate the enhancement of photoprotective energy dissipation of both photosystems in wild-type Arabidopsis thaliana after 6 h exposure to fluctuating light as compared with constant light conditions. This acclimation response to fluctuating light was hampered in a triple mutant lacking the thylakoid ion transport proteins KEA3, VCCN1, and CLCe, leading to photoinhibition of photosystem I. Transcriptome analysis revealed upregulation of genes involved in biotic stress and defense responses in both genotypes after exposure to fluctuating as compared with constant light, yet these responses were demonstrated to be largely upregulated in triple mutant already under constant light conditions compared with wild type. The current study illustrates the rapid acclimation of plants to fluctuating light, including photosynthetic, transcriptomic, and metabolic adjustments, and highlights the connection among thylakoid ion transport, photosynthetic energy balance, and cell signaling.

Plant species with larger extrafloral nectaries produce better quality nectar when needed and interact with the best ant partners.

Few studies have explored the phenotypic plasticity of nectar production on plant attractiveness to ants. Here, we investigate the role of extrafloral nectary (EFN) size on the productivity of extrafloral nectar in three sympatric legume species. We hypothesized that plant species with larger EFNs (i) have higher induced nectar secretion after herbivory events, and (ii) are more likely to interact with more protective (i.e. dominant) ant partners. We target 90 plants of three Chamaecrista species in the field. We estimated EFN size and conducted field experiments to evaluate any differences in nectar traits before and after leaf damage to investigate the phenotypic plasticity of nectar production across species. We conducted multiple censuses of ant species feeding on EFNs over time. Plant species increased nectar descriptors after leaf damage, but in different ways. Supporting our hypothesis, C. duckeana, with the largest EFN size, increased all nectar descriptors, with most intense post-herbivory-induced response, taking its place as the most attractive to ants, including dominant species. EFN size variation was an excellent indicator of nectar productivity across species. The higher control over reward production in plants with larger sized EFNs reflects an induction mechanism under damage that reduces costs and increases the potential benefits of indirect biotic defences.

Combining elicitor treatment of chitosan, methyl jasmonate, and cyclodextrin to induce the generation of immune response bioactive peptides in peanut hairy root culture

The endogenous peptides from peanut hairy root culture were induced upon elicitor treatment with chitosan (CHT), methyl jasmonate (MeJA), and cyclodextrin (CD): CHT+MeJA+CD. The peptides secreted into the liquid culture medium play an important role in plant signaling and stress responses. By performing gene ontology (GO) analysis, a number of plant proteins involved in biotic and abiotic defense responses were identified, such as endochitinase, defensin, antifungal protein, cationic peroxidase and Bowman-Birk type protease inhibitor A-II. The bioactivity of 14 peptides synthesized from secretome analysis was determined. Peptide BBP1–4, derived from the diverse region of Bowman-Birk type protease inhibitor, displayed high antioxidant activity and mimicked the property of chitinase and β-1,3-glucanase enzymes. The antimicrobial activity against S. aureus, S. typhimurium, and E. coli was evidenced with different peptide concentrations. Additionally, peptide BBP1–4 has the potential to be a useful candidate for an immune response property, as it was found to increase the expression of some pathogenesis-related (PR) proteins and stilbene biosynthesis genes in peanut hairy root tissues. The findings indicate that secreted peptides may play a role in plant responses to both abiotic and biotic stresses. These peptides, which possess bioactive properties, could be considered as potential candidates for use in the pharmaceutical, agricultural, and food industries.

Transcriptomic Analysis Revealed Key Defense Genes and Signaling Pathways Mediated by the Arabidopsis thaliana Gene SAD2 in Response to Infection with Pseudomonas syringae pv. Tomato DC3000.

Nucleocytoplasmic transport receptors play key roles in the nuclear translocation of disease resistance proteins, but the associated mechanisms remain unclear. The Arabidopsis thaliana gene SAD2 encodes an importin β-like protein. A transgenic Arabidopsis line overexpressing SAD2 (OESAD2/Col-0) showed obvious resistance to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) compared to the wild type (Col-0), but the knockout mutant sad2-5 was susceptible. Transcriptomic analysis was then performed on Col-0, OESAD2/Col-0, and sad2-5 leaves at 0, 1, 2, and 3 days post-inoculation with Pst DC3000. A total of 1825 differentially expressed genes (DEGs) were identified as putative biotic stress defense genes regulated by SAD2, 45 of which overlapped between the SAD2 knockout and overexpression datasets. Gene Ontology (GO) analysis indicated that the DEGs were broadly involved in single-organism cellular metabolic processes and in response to stimulatory stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) biochemical pathway analysis revealed that many of the DEGs were associated with the biosynthesis of flavonoids and other specialized metabolites. Transcription factor analysis showed that a large number of ERF/AP2, MYB, and bHLH transcription factors were involved in SAD2-mediated plant disease resistance. These results provide a basis for future exploration of the molecular mechanisms associated with SAD2-mediated disease resistance and establish a set of key candidate disease resistance genes.

Data science approaches provide a roadmap to understanding the role of abscisic acid in defence

Abscisic acid (ABA) is a plant hormone well known to regulate abiotic stress responses. ABA is also recognised for its role in biotic defence, but there is currently a lack of consensus on whether it plays a positive or negative role. Here, we used supervised machine learning to analyse experimental observations on the defensive role of ABA to identify the most influential factors determining disease phenotypes. ABA concentration, plant age and pathogen lifestyle were identified as important modulators of defence behaviour in our computational predictions. We explored these predictions with new experiments in tomato, demonstrating that phenotypes after ABA treatment were indeed highly dependent on plant age and pathogen lifestyle. Integration of these new results into the statistical analysis refined the quantitative model of ABA influence, suggesting a framework for proposing and exploiting further research to make more progress on this complex question. Our approach provides a unifying road map to guide future studies involving the role of ABA in defence.

Ineffectiveness of ants in protecting two sympatric myrmecophilous plants against endophytic beetles

AbstractExtrafloral nectarized plants attract ants, which may protect them against herbivory and increase plant fruit set production. In some cases, however, ants are ineffective against herbivores. Such events occur, for instance, when herbivores present adaptations to avoid ant predation. Thus, the outputs of these interactions depend on factors such as ant identity, plant phenology and herbivore features. Here, we investigated the endophytic florivorous beetles' impact on the reproductive success of their host plants, two sympatric Banisteriopsis (Malpighiaceae) species, depending on the action of extrafloral nectaries (EFNs) visiting ants. We experimentally manipulated the presence of ants and herbivores on B. malifolia and B. laevifolia species during their reproductive period to test the effectiveness of ants‐EFNs mutualism on plant fruit set production. We performed treatments where three similar inflorescences were selected to be (I) control branch, with no manipulations, (II) beetle‐free branch, isolated with textile cover and (III) ant‐free branch, isolated at the base with atoxic wax. We hypothesized that endophytic herbivores have a negative impact on the plant reproductive success because they escape the action of ants (biotic defences). As a result, we observed (i) that florivorous Anthonomus beetles have a negative impact on Banisteriopsis reproductive success; (ii) ants fail in protecting plants against floral endophytic beetles; and (iii) most of the results were species‐specific. Our results indicate that these systems present very conditional outcomes that depend on the intrinsic factors of each plant species.

Role of Salicylic Acid in Combating Heat Stress in Plants: Insights into Modulation of Vital Processes.

In the present era of climate change and global warming, high temperatures have increased considerably, posing a threat to plant life. Heat stress affects the biochemistry, physiology and molecular makeup of the plant by altering the key processes, i.e., photosynthesis, respiration and reproduction which reduces its growth and development. There is a dire need to manage this problem sustainably for plant conservation as well as the food security of the human population. Use of phytohormones to induce thermotolerance in plants can be a sustainable way to fight the adversities of heat stress. Phytohormone-induced thermotolerance proves to be a compelling approach to sustainably relieve the damaging effects of heat stress on plants. Salicylic acid (SA) is an essential molecule in biotic and abiotic defense response signal transduction pathways. When supplied externally, it imparts heat stress tolerance to the plants by different means, viz., increased Heat Shock Proteins (HSP) production, Reactive oxygen species (ROS) scavenging, protection of the reproductive system and enhancing photosynthetic efficiency. The effect of SA on plants is highly dependent on the concentration applied, plant species, plant age, type of tissues treated, and duration of the treatment. The present review paper summarizes the mechanism of thermotolerance induced by salicylic acid in plants under heat stress conditions. It includes the regulatory effects of SA on heat shock proteins, antioxidant metabolism, and maintenance of Ca2+ homeostasis under heat stress. This review combines the studies conducted to elucidate the role of SA in the modulation of different mechanisms which lead to heat stress tolerance in plants. It discusses the mechanism of SA in protecting the photosynthetic machinery and reproductive system during high-temperature stress.

Climate and the biotic community structure plant resistance across biogeographic groups of yellow monkeyflower.

Characterizing correlates of phytochemical resistance trait variation across a landscape can provide insight into the ecological factors that have shaped the evolution of resistance arsenals. Using field-collected data and a greenhouse common garden experiment, we assessed the relative influences of abiotic and biotic drivers of genetic-based defense trait variation across 41 yellow monkeyflower populations from western and eastern North America and the United Kingdom. Populations experience different climates, herbivore communities, and neighboring vegetative communities, and have distinct phytochemical resistance arsenals. Similarities in climate as well as herbivore and vegetative communities decline with increasing physical distance separating populations, and phytochemical resistance arsenal composition shows a similarly decreasing trend. Of the abiotic and biotic factors examined, temperature and the neighboring vegetation community had the strongest relative effects on resistance arsenal differentiation, whereas herbivore community composition and precipitation have relatively small effects. Rather than simply controlling for geographic proximity, we jointly assessed the relative strengths of both geographic and ecological variables on phytochemical arsenal compositional dissimilarity. Overall, our results illustrate how abiotic conditions and biotic interactions shape plant defense traits in natural populations.

Genetic architecture of multiple mutualisms and mating system in Turnera ulmifolia.

Plants often associate with multiple arthropod mutualists. These partners provide important services to their hosts, but multiple interactions can constrain a plant's ability to respond to complex, multivariate selection. Here, we quantified patterns of genetic variance and covariance among rewards for pollination, biotic defence and seed dispersal mutualisms in multiple populations of Turnera ulmifolia to better understand how the genetic architecture of multiple mutualisms might influence their evolution. We phenotyped plants cultivated from 17 Jamaican populations for several mutualism and mating system-related traits. We then fit genetic variance-covariance (G) matrices for the island metapopulation and the five largest individual populations. At the metapopulation level, we observed significant positive genetic correlations among stigma-anther separation, floral nectar production and extrafloral nectar production. These correlations have the potential to significantly constrain or facilitate the evolution of multiple mutualisms in T.ulmifolia and suggest that pollination, seed dispersal and defence mutualisms do not evolve independently. In particular, we found that positive genetic correlations between floral and extrafloral nectar production may help explain their stable coexistence in the face of physiological trade-offs and negative interactions between pollinators and ant bodyguards. Locally, we found only small differences in G among our T.ulmifolia populations, suggesting that geographic variation in G may not shape the evolution of multiple mutualisms.

Metabolic engineering to enhance the accumulation of bioactive flavonoids licochalcone A and echinatin in Glycyrrhiza inflata (Licorice) hairy roots.

Echinatin and licochalcone A (LCA) are valuable chalcones preferentially accumulated in roots and rhizomes of licorice (Glycyrrhiza inflata). The licorice chalcones (licochalcones) are valued for their anti-inflammatory, antimicrobial, and antioxidant properties and have been widely used in cosmetic, pharmaceutical, and food industries. However, echinatin and LCA are accumulated in low quantities, and the biosynthesis and regulation of licochalcones have not been fully elucidated. In this study, we explored the potential of a R2R3-MYB transcription factor (TF) AtMYB12, a known regulator of flavonoid biosynthesis in Arabidopsis, for metabolic engineering of the bioactive flavonoids in G. inflata hairy roots. Overexpression of AtMYB12 in the hairy roots greatly enhanced the production of total flavonoids (threefold), echinatin (twofold), and LCA (fivefold). RNA-seq analysis of AtMYB12-overexpressing hairy roots revealed that expression of phenylpropanoid/flavonoid pathway genes, such as phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), and flavanone 3'-hydroxylase (F3'H), is significantly induced compared to the control. Transient promoter activity assay indicated that AtMYB12 activates the GiCHS1 promoter in plant cells, and mutation to the MYB-binding motif in the GiCHS1 promoter abolished activation. In addition, transcriptomic analysis revealed that AtMYB12 overexpression reprograms carbohydrate metabolism likely to increase carbon flux into flavonoid biosynthesis. Further, AtMYB12 activated the biotic defense pathways possibly by activating the salicylic acid and jasmonic acid signaling, as well as by upregulating WRKY TFs. The transcriptome of AtMYB12-overexpressing hairy roots serves as a valuable source in the identification of potential candidate genes involved in LCA biosynthesis. Taken together, our findings suggest that AtMYB12 is an effective gene for metabolic engineering of valuable bioactive flavonoids in plants.

The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree.

The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The tree Prosopis cineraria is native to the Near East and Indian subcontinent, where it thrives in very hot desert environments. To develop a tool to better understand desert plant adaptation mechanisms, we sequenced the P. cineraria genome to near-chromosomal assembly, with a total sequence length of ~691 Mb. We predicted 77,579 gene models (76,554 CDS, 361 rRNAs and 664 tRNAs) from the assembled genome, among them 55,325 (~72%) protein-coding genes that were functionally annotated. This genome was found to consist of over 58% repeat sequences, primarily long terminal repeats (LTR-)-retrotransposons. We find an expansion of terpenoid metabolism genes in P. cineraria and its relative Prosopis alba, but not in other legumes. We also observed an amplification of NBS-LRR disease-resistance genes correlated with LTR-associated retrotransposition, and identified 410 retrogenes with an active burst of chimeric retrogene creation that approximately occurred at the same time of divergence of P. cineraria from a common lineage with P. alba~23 Mya. These retrogenes include many biotic defense responses and abiotic stress stimulus responses, as well as the early Nodulin 93 gene. Nodulin 93 gene amplification is consistent with an adaptive response of the species to the low nitrogen in arid desert soil. Consistent with these results, our differentially expressed genes show a tissue specific expression of isoprenoid pathways in shoots, but not in roots, as well as important genes involved in abiotic salt stress in both tissues. Overall, the genome sequence of P. cineraria enriches our understanding of the genomic mechanisms of its disease resistance and abiotic stress tolerance. Thus, it is a very important step in crop and legume improvement.