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Biology, Plant Sciences; Linum usitatissimum, GWAS, seed mucilage content, seed hull content, single nucleotide poymosphism (SNP)
Online: 14 August 2018 (16:42:57 CEST)
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New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million SNP markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 Kb. Seven and four QTL were identified for MC and HC, respectively. Promising candidate genes included Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17 and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE that have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana were identified. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal flaxseed cultivars for food and feed by genomic-based breeding.
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Biology, Plant Sciences; Cudratricusxanthone L; Cudrania tricuspidata; Neuroinflammation; Nuclear factor-kappa B (NF-κB); Mitogen-activated protein kinase (MAPK)
Online: 9 August 2018 (20:43:24 CEST)
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Neuroinflammatory responses are implicated in the pathogenesis of neurodegenerative diseases. In neurodegenerative diseases, neuroinflammatory reactions to neuronal injury are modulated by microglial cells, which are vital innate immune cells in the central nervous system. Activated microglial cells release proinflammatory cytokines, mediators, and neurotoxic factors that induce fatal neuronal injury. The present study investigated the anti-neuroinflammatory effects of cudratricusxanthone L (1), which was isolated from Cudrania tricuspidata. This compound reduced the levels of lipopolysaccharide-stimulated inflammatory mediators and cytokines, including nitric oxide, prostaglandin E2, interleukin (IL)-1β, tumor necrosis factor-α, IL-6, and IL-12. These effects suggested that cudratricusxanthone L (1) suppressed the nuclear factor-kappa B (NF-κB) signaling pathway. Specifically, cudratricusxanthone L (1) also attenuated the phosphorylation of Jun kinase and inhibited p38 mitogen-activated protein kinase (MAPK) signaling in BV2 and rat primary microglial cells. These results indicated that cudratricusxanthone L (1) effectively repressed neuroinflammatory processes in BV2 and rat primary microglial cells by inhibiting NF-κB and the MAPK signaling pathway.
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Shoko Hasegawa,
Takuya Tsutsumi,
Shunsuke Fukushima,
Yoshihiro Okabe,
Junna Saito,
Mina Katayama,
Masato Shindo,
Yusuke Yamada,
Koichiro Shimomura,
Kaori Yoneyama,
Kohki Akiyama,
Koh Aoki,
Tohru Ariizumi,
Hiroshi Ezura,
Shinjiro Yamaguchi,
Mikihisa Umehara
Biology, Plant Sciences; carotenoid cleavage dioxygenase 8; Orobanche minor; Phelipanche aegyptiaca; shoot branching; Solanum lycopersicum; strigolactones
Online: 8 August 2018 (15:24:04 CEST)
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Strigolactones (SLs), a group of plant hormones, induce germination of root-parasitic plants and inhibit shoot branching in many plants. Shoot branching is an important trait that affects the number and quality of flowers and fruits. Root-parasitic plants such as Phelipanche spp. infect tomato roots and cause economic damage in Europe and North Africa. Thus, resistant tomato cultivars are needed. In this study, we found carotenoid cleavage dioxygenase 8-defective mutants of Micro-Tom tomato (slccd8) by the “targeting induced local lesions in genomes” (TILLING) method. The mutants showed excess branching, which was suppressed by exogenously applied SL. Grafting shoot scions of the slccd8 mutants onto wild-type (WT) rootstocks restored normal branching in the scions. The levels of endogenous orobanchol and solanacol in WT were enough detectable, whereas that in the slccd8 mutants were below the detection limit of quantification analysis. Accordingly, root exudates of the slccd8 mutants hardly stimulated seed germination of root parasitic plants. In addition, SL deficiency did not critically affect the fruit traits of Micro-Tom. Using a rhizotron system, we also found that Phelipanche aegyptiaca infection was lower in the slccd8 mutants than in wild-type Micro-Tom because of the low germination. We propose that the slccd8 mutants might be useful as new tomato lines resistant to P. aegyptiaca.
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Biology, Plant Sciences; DAMPs; alarmins; innate immune response; plants; phylogeny; in silico
Online: 26 July 2018 (16:08:54 CEST)
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In plants and animals, endogenous biological molecules, termed damage-associated molecular patterns (DAMPs) or alarmins, are released by damaged, stressed or dying cells following abiotic stress such as radiation and drought stress. In turn, a cascade of downstream signaling events is initiated leading to the up-regulation of defense-related genes. In the present study, in an effort to investigate the conservation status of the molecular mechanisms implicated in the danger signaling, thorough in silico phylogenetic and structural analyses of the effector biomolecules were performed in taxonomically diverse plant species. On the basis of our results, the defense mechanisms appear to be largely conserved within the plant kingdom. Of note is our finding that the sequence and/or function of several components of these mechanisms were found to be conserved in animals, as well.
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Biology, Plant Sciences; Seed coat; pericarps; floral bracts; glumes; dead organs enclosing embryos; seed germination; seedling establishment; hydrolytic enzymes; ROS detoxifying enzymes; cell wall modification enzymes; nutrients; phytohormones; nucleases; chitinases; Brassicaceae; Poaceae
Online: 26 July 2018 (09:53:41 CEST)
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Plants have evolved a variety of dispersal units whereby the embryo is enclosed by various dead protective layers derived from maternal organs of the reproductive system including seed coats (integuments), pericarps (ovary wall, e.g., indehiscent dry fruits) as well as floral bracts (e.g. glumes) in grasses. Commonly, dead organs enclosing embryos (DOEEs) are assumed to provide a physical shield for embryo protection and means for dispersal in the ecosystem. In this review article, we will highlight recent studies showing that DOEEs of various species across families also have the capability for long-term storage of various substances including active proteins (hydrolases, ROS detoxifying enzymes), nutrients and metabolites that have the potential to support the embryo during storage in the soil and assist in germination and seedling establishment. We discuss a possible role for DOEEs as natural coatings capable of ‘engineering’ the seed microenvironment for the benefit of the embryo, the seedling and the growing plant.
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Biology, Plant Sciences; aquaporin; pollen hydration; stigma; PIP2;5; arabidopsis
Online: 25 July 2018 (06:24:50 CEST)
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In flowering plants with dry stigmas, pollen hydration involves water movement, which may be facilitated by aquaporins. To explore the possibility underlying this biological process, we identified and characterized a mutant with a T-DNA insertion in PIP2;5, which encodes an aquaporin with water channel activity in the PIP2 subfamily. We monitored the pollination process (pollen hydration, germination, and pollen tube growth) of wild type pollen on stigmas of the mutant and wild type. Pollen hydration was postponed on the stigmas of the mutant, compared with that on wild type stigmas. However, pollen tube germination and growth was unaffected in the mutant. The PIP2;5 protein was located in the cell plasma membrane and was preferentially expressed in the stigma. Based on our results, we concluded that PIP2;5 might play an important role in water movement during pollen hydration.
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Yingzhong Zhang,
Liangbo Zhang,
Jing Wang,
Xuxiao Tang,
Hong Wu,
Minghuai Wang,
Wu Zeng,
Qihui Mo,
Yongquan Li,
Jianwei Li,
Yijuan Huang,
Baohua Xu,
Mengyu Zhang
Biology, Plant Sciences; Near infrared reflectance spectroscopy; Camellia seeds kernel; Oil content; Moisture content
Online: 23 July 2018 (21:12:39 CEST)
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A fast and effective determination method of different species of vegetable seeds oil is vital in the plant oil industry. The near-infrared reflectance spectroscopy (NIRS) method was developed in this study to massively analyze the oil and moisture contents of Camellia gauchowensis Chang and C. semiserrata Chi seeds kernels. In the prediction models of NIRS, the levels of accuracy obtained were sufficient for C. gauchowensis Chang and C. semiserrata Chi, the correlation coefficient of which oil were 0.983 and 0.962, respectively, while which of moisture were 0.937 and 0.907, respectively. The near infrared spectrum of crush seeds kernels was more precise compared to intact kernels. Based on the calibration models of the two Camellia species, the NIRS predictive oil contents of C. gauchowensis Chang and C. semiserrata Chi seeds kernels were 48.71 ± 8.94% and 31.71 ± 7.39%, respectively, and the NIRS predictive moisture contents were 4.39 ± 1.08% and 3.49 ± 0.71%, respectively. Compared with the traditional chemical measurement, the rapid, precise measurement of oil and moisture of C. gauchowensis Chang and C. semiserrata Chi seeds kernels can be actualized by NIRS method.
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Biology, Plant Sciences; novel lncRNA; lncRNA conservation; copaifera; epigenetics; adaptive response
Online: 20 July 2018 (04:31:16 CEST)
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LncRNA are involved in multiple regulatory pathways, its versatile mode of action has disclosed a new layer in gene regulation. They are reportedly modulated during plant development, with specific tissue functions and in response to stresses. In this study, we analyzed LncRNA from leave samples collected from the legume Copaifera langsdorffii (copaiba) from two divergent ecosystems: Cerrado (CER) and Atlantic Rain Forest (ARF). We identified 8020 novel lncRNAs, from which 2893 transcripts were regulated above 2-fold and 566 above 5-folds in either condition. This putative lncRNA set was compared with seven Fabaceae genomes, of which 1747 and 1879 transcripts (from ARF and CER, respectively) aligned to at least two genomes. Further, 2194 copaiba lncRNAs were successfully mapped to at least one of six Fabaceae transcriptomes. The secondary structures of the lncRNAs that were conserved and differentially expressed between the populations were predicted using in silico methods. Our results indicate the potential involvement of lncRNAs in the adaptation of C. langsdorffii to two different biomes.
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Biology, Plant Sciences; bioelectrochemical systems (BES); electroactive bacteria (EAB); extracelullar electron transfer (EET); microbial fuel cells (MFC); treatment wetlands
Online: 20 July 2018 (04:03:11 CEST)
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Microbial electrochemical technologies (MET) rely on the presence of the metabolic activity of electroactive bacteria for the use of solid-state electrodes for oxidizing different kind of compound, that could lead to the synthesis of chemicals, bioremediation of polluted matrices, the treatment of contaminants of interest, as well as the recovery of energy. Keeping in mind those possibilities, since the beginning of the present century, there has been a growing interest in the use of electrochemical technologies for wastewater treatment, and if possible with simultaneous power generation. In the last years, there has been a growing interest to explore the possibility of merging MET with constructed wetlands, to offer a new option of intensified wetland system that could keep a high performance with a lower footprint. Based on that interest, this paper explains the general principles of MET, and the different known extracellular electron transfer mechanisms ruling the interaction between electroactive bacteria and potential solid-state electron acceptors. Also, the adoption of those principles for the development of MET set-ups for simultaneous wastewater treatment and power generation, and the challenges that the technology face. Ultimately, the most recent developments in set-ups that merges MET with constructed wetlands are presented and discussed.
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Biology, Plant Sciences; bread wheat; correlations, gamma, grain nutrients concentrations; mutation, phytic acid; metals bioavailability
Online: 9 July 2018 (15:39:51 CEST)
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Metal, primarily Fe and Zn, deficiencies affect over half of the world's population. Human diets with prevalent cereal products cause micronutrient malnutrition. Biofortification is one of the most effective approaches to alleviate malnutrition. Spring wheat genetically stable (M7) mutant lines developed with 100 and 200 Gy gamma treatments to broaden genetic variation and search for new resources were analyzed for nutritionally important minerals (Ca, Mg, K, Fe, and Zn), their bioavailability, and grain protein content (GPC). The variation was 172.3–883.0 mg/kg for Ca, 472.9–1088 mg/kg for Mg, 3128.6–5487.5 mg/kg for K, 40.9–89.0 mg/kg for Fe, and 22.2–89.6 mg/kg for Zn. In mutant lines, among the investigated minerals, the highest increases in concentrations were observed in Fe, Zn, and Ca when compared to the parent. Some mutant lines, mostly in the 100 Gy-derived germplasm, had two to three times higher Fe, Zn, and Ca concentrations, lower phytic acid concentration (1.4–2.1 times), and 6.5–7% higher GPC compare to the parent. Variation was detected for the Ca:Phy, Mg :Phy, Phy:K, Phy:Fe, and Phy:Zn molar ratios, (1.27–10.41, 5.05–18.68, 1.66–4.87, 1.40–5.32 and 1.78–11.78, respectively). The results showed how the genetic variation could be generated through radiation and be useful to develop biofortification by micronutrient varieties with their appropriate bioavailability to overcome malnutrition.
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Biology, Plant Sciences; comparative proteomics analysis; CIPK14; WHIRLY1/WHIRLY3; protein metabolism
Online: 6 July 2018 (08:51:11 CEST)
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Leaf variegation pale yellowing is observed in the Calcineurin B-Like-Interacting Protein Kinase14 (CIPK14) overexpression line (oeCIPK14) and double knockout WHIRLY1/WHIRLY3 (why1/3) lines of Arabidopsis, the distribution of WHIRLY1 (WHY1) protein between plastids and the nucleus are affected by the phosphorylation of WHY1 by CIPK14. To elucidate the coregulation of CIPK14 and WHIRLY1/WHIRLY3 mediated leaf pale yellowing, a differential proteomic analysis is conducted between the oeCIPK14 variegated (oeCIPK14-var) line, why1/3 variegated (why1/3-var) line and wild type (WT). More than 800 protein spots are distinguished on each gel, 67 differential abundance proteins (DAPs) are identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF-MS), of which, 34 DAPs are in the oeCIPK14-var, 33 DAPs are in the why1/3-var compared to WT. Five overlapping proteins differentially change both in the oeCIPK14-var and in the why1/3-var. They are ATP-dependent Clp protease proteolytic subunit-related protein 3 (ClpR3), Ribulose bisphosphate carboxylase large chain (RBL), Beta-amylase 3 (BAM3), Ribosome-recycling factor (RRF), Ribulose bisphosphate carboxylase small chain (RBS). Bioinformatics analysis show that most of DAPs are involved in photosynthesis, defense and antioxidation pathway, protein metabolism, amino acid metabolism, energy metabolism, malate biosynthesis, lipid metabolism and transcription. Thus, the photosystem parameters are measured that the content of chlorophyll, the photochemical efficiency of PSⅡ (Fv/Fm), and electron transport rates (ETR) decrease in the why1/3-var and oeCIPK14-var, but the non-photochemical quenching (NPQ) increases. Both mutants show high sensitivity to strong light. Based on the annotation of DAPs from both why1/3-var and oeCIPK14-var lines, we conclude that CIPK14 phosphorylation mediated WHY1 deficiency in plastids is related to impairment of protein metabolism leading to chloroplast dysfunction.
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Biology, Plant Sciences; abiotic stresses; GWAS; ionomics; omics; phenomics; QTL
Online: 28 June 2018 (04:41:19 CEST)
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Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence, and heavy metals. The effective management at molecular level is mandatory for thorough understanding of plant response to abiotic stress. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in wheat. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in wheat. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in wheat. This review also provides a comprehensive catalog of available online omic resources for wheat and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in wheat.
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Biology, Plant Sciences; Keywords: Bacillus amyloliquefaciens, Chitinase, Defense enzymes; Biological control
Online: 19 June 2018 (15:56:47 CEST)
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To investigate whether the ech42 gene in Clonostachys rosea can improve the biocontrol efficacy of Bacillus amyloliquefaciens and its molecular mechanism.Compared to the wild type, the B. amyloliquefaciens transformed with the ech42 gene exhibited a higher chitinase activity. The B. amyloliquefaciens-ech42 also showed a significantly higher biocontrol efficiency against B. cinerea when tomato plants were pre-treated with amyloliquefaciens-ech42. No significant difference of control efficiency was observed between the wild type and amyloliquefaciens-ech42 when tomato plants were first infected by B. cinerea. In addition, the activity of the defense-related enzyme polyphenol oxidase, but not superoxide dismutase was significantly higher in amyloliquefaciens-ech42 than in the wild type.The ech42 enhances the Bacillus amyloliquefaciens biocontrol efficiency by increasing the capacity of protection/prevention to plants, rather treating/killing the pathogens.
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Igor Koloniuk,
Thanuja Thekke-Veetil,
Jean-Sébastien Reynard,
Irena Mavrič Pleško,
Jaroslava Přibylová,
Justine Brodard,
Isabelle Kellenberger,
Tatiana Sarkisova,
Josef Špak,
Janja Lamovšek,
Sebastien Massart,
Thien Ho,
Joseph Postman,
Ioannis Tzanetakis
Biology, Plant Sciences; Ribes; currant; closterovirus; recombinants/recombination
Online: 15 June 2018 (14:40:33 CEST)
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Five isolates of a new putative member of the genus Closterovirus, tentatively named blackcurrant leafroll associated virus 1 (BcLRaV-1), were identified in currant. The 17 kb long genome of BcLRaV-1 contained 10 open reading frames (ORFs). The replication associated polyprotein has two papain-like leader proteases, a methyltransferase, a helicase and an RNA-dependent RNA polymerase domain. Additional ORFs coded for heat shock protein 70 homolog, heat shock protein 90 homolog, two divergent copies of coat protein, and three accessory proteins without identifiable functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus and recombination analysis of the isolates showed clear evidences of intraspecies recombination.
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Biology, Plant Sciences; morphogenesis, cell wall protein, Hechtian oscillator, calcium signalling, H+ ATPase
Online: 15 June 2018 (14:15:29 CEST)
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Morphogenesis remains a riddle, wrapped in a mystery, inside an enigma. It remains a formidable problem viewed from many different perspectives of morphology, genetics, and computational modelling. We propose a biochemical reductionist approach that shows how both internal and external physical forces contribute to plant morphogenesis via mechanical stress-strain transduction from the primary cell wall tethered to the plasma membrane by a specific arabinogalactan protein (AGP). The resulting stress vector with direction defined by Hechtian adhesion sites, has a magnitude of a few picoNewtons amplified by a hypothetical Hechtian growth oscillator. This paradigm shift involves stress activated plasma membrane Ca2+channels and auxin-activated H+-ATPase. The proton pump dissociates periplasmic AGP-glycomodules that bind Ca2+. Thus, as the immediate source of cytosolic Ca2+ an AGP-Ca2+ capacitor directs vectorial exocytosis of cell wall precursors and auxin efflux (PIN) proteins. In toto these components comprise the Hechtian Oscillator and also the gravisensor. Thus interdependent auxin and Ca2+ morphogen gradients account for the predominance of AGPs. The size and location of a cell surface AGP-Ca2+ capacitor is essential to differentiation and explains AGP correlation with all stages of morphogenetic patterning from embryogenesis to root and shoot. Finally, evolutionary origins of the Hechtian Oscillator in the unicellular Chlorophycean algae reflect the ubiquitous role of chemiosmotic proton pumps that preceded DNA at the dawn of life.
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Biology, Plant Sciences; epigenetics; differentially methylated markers (DMMs); LEAVES; roots; DNA methylation; salinity stress; barley
Online: 15 June 2018 (06:10:53 CEST)
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Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated with the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here, we assessed the extent of salt-induced alterations of DNA methylation in barley and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, to seek genotype independent salt-induced changes in DNA methylation. Salt stress caused increased methylation in leaves but diminished methylation in roots with a higher number of changes in leaves than in roots, indicating that salt induced changes to global methylation are organ specific. Differentially Methylated Markers (DMMs) were mostly located in close proximity to repeat elements, but also in 1094 genes, of which many possessed gene ontology (GO) terms associated with plant responses to stress. Identified markers have potential value as sentinels of salt stress and provide a starting point to allow understanding of the functional role of DNA methylation in facilitating barley’s response to this stressor.
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Biology, Plant Sciences; epigenetics; H3K9 methylation; H3K4 methylation; DNA methylation; seasonal climate change; summer dormancy; heat shock proteins; ribosomal proteins; Zygophyllum dumosum Boiss
Online: 4 June 2018 (12:49:59 CEST)
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Plants thriving in desert environments are suitable for studying mechanisms for plant survival under extreme seasonal climate variation. Zygophyllum dumosum Boiss, like many other Zygophyllaceae species, displays a unique epigenetic mechanism whereby the repressive markers di- and tri-methyl of H3K9 do not exist. We studied epigenetic mechanisms underlying seasonal growth cycles in Z. dumosum and their association with factors regulating basic cell functions. We showed strong association between rainfall and seasonal growth and the epigenetic marker of dimethyl H3K4, which disappears on entry into the dry season and the acquisition of dormant state. DNA methylation is not affected by lack of H3K9 di and tri methyl and changes in methylation pattern are apparent on entry into the dry season. Proteome analysis of acid soluble fractions revealed extensive reduction in ribosomal proteins and in proteins involved in chloroplasts and mitochondria activities during the dry seasons concomitantly with up-regulation of molecular chaperone HSPs. Our results highlight mechanisms underlying Z. dumosum adaptation to seasonal climate variation. Particularly, summer dormancy is associated with loss of the permissive epigenetic marker dimethyl H3K4, which might facilitate genome compaction, concomitantly with significant reduction in proteins involved in basic cell functions (i.e., protein synthesis, photosynthesis and respiration).
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Biology, Plant Sciences; heavy metals; dyer´s greenweed; elicitation; exudation
Online: 4 June 2018 (10:13:25 CEST)
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Family Fabaceae traditionally serves as food and herbal remedies source. Several plants are already used for menopausal symptoms treatment based on a presence of typical secondary metabolites, isoflavones. Beside soybean and clovers, isoflavones could be produced by other plants or in vitro cultures. This type of production can be further enhanced by elicitation that stimulates metabolites biosynthesis via stress reaction. Vanadium compounds have been already described as potential elicitors and the aim of this study was to determine an impact of NH4VO3 and VOSO4 solutions on isoflavones production in Genista tinctoria L. cell cultures. The significant increase of isoflavones content such as genistin, genistein or formononetin was measured in a nutrient medium or dry mass after NH4VO3 treatment for 24 or 48 hours. The possible transport mechanism of isoflavones was also evaluated. An incubation with different transport inhibitors prior elicitation took effect on isoflavones content in the medium. However, there was non-ended result for particular metabolites such as genistein and daidzein, where ABC or alternatively MATE proteins can participate. Possible elicitation by some inhibitors was also discussed as result of their pleiotropic effect. Despite this outcome, the determining of transport mechanism is important step for identification of specific transporter.
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Biology, Plant Sciences; epigenomics, hordeum vulgare, leaf, root, tissue-specific methylation, developmental epigenomics
Online: 25 April 2018 (16:53:56 CEST)
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The barley (Hordeum vulgare) genome comprises over 32,000 genes, with differentiated cells expressing only a subset of genes; the remainder being silent. Mechanisms by which tissue-specific genes are regulated are not entirely understood, although DNA methylation is likely to be involved. DNA methylation patterns are not static during plant development, but it is still unclear whether different organs possess distinct methylation profiles. Methylation-sensitive GBS was used to generate DNA methylation profiles for roots, leaf-blades and leaf-sheaths from five barley varieties, using seedlings at the three-leaf stage. Differentially Methylated Markers (DMMs) were characterised by pairwise comparisons of roots, leaf-blades and leaf-sheaths of three different ages. While very many DMMs were found between roots and leaf parts, only a few existed between leaf-blades and leaf-sheaths, with differences decreasing with leaf rank. Organ-specific DMMs appeared to target mainly repeat regions, implying that organ differentiation partially relies on the spreading of DNA methylation from repeats to promoters of adjacent genes. Furthermore, the biological functions of differentially methylated genes in the different organs correlated with functional specialisation. Our results indicate that different organs do possess diagnostic methylation profiles and suggest that DNA methylation is important for both tissue development and differentiation and organ function.
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Biology, Plant Sciences; gas exchange; leaf canopy temperature; life forms; thermography; woody vines
Online: 20 April 2018 (11:55:08 CEST)
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Leaf temperature (Tleaf) influences photosynthesis and respiration. Currently, there is a growing interest on including lianas in productivity models due to their increasing abundance, and their detrimental effects on net primary productivity in tropical environments. Therefore, understanding the differences of Tleaf between lianas and trees is important for future of forest on whole ecosystem productivity. Here we determined the displayed leaf temperature (Td= Tleaf – ambient temperature) of several species of lianas and their host trees during ENSO and non-ENSO years to evaluate if the presence of lianas affects the Td of their host trees, and if leaves of lianas and their host trees exhibit differences in Td. Our results suggest that close to midday, the presence of lianas does not affect the Td of their host trees; however, lianas tend to have higher values of Td than their hosts across seasons, in both ENSO and non-ENSO years. Although lianas and trees tend to have similar physiological-temperature responses, differences in Td could lead to significant differences in rates of photosynthesis and respiration based temperature response curves. Future models should thus consider differences in leaf temperature between these life forms to achieve robust predictions of productivity.
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Biology, Plant Sciences; bacterial artificial chromosomes; RNAseq; genetic map; transposable element; gene density
Online: 10 April 2018 (10:49:41 CEST)
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Many dioecious plants have sex chromosomes that are cytologically heteromorphic, but about half of species lack cytological differences between males and females and are thus homomorphic. Very little is known about the size and content of the non-recombining sex-determining region (SDR) in these species. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, which has homomorphic sex chromosomes and shows signatures of mild Y-chromosome degeneration. We used RNAseq to identify new Y-linked markers for M. annua. Twelve of 24 transcripts with male-specific and male-biased expression could only be PCR-amplified from males and are thus Y-linked. We found a further six Y-linked sequences that were present in males but not females using genome capture data from multiple populations. We used the Y-linked sequences to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequence, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests it is enriched for repeats, has a low gene density and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which is estimated to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, especially given the small genome size of M. annua. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Biology, Plant Sciences; Hippophae rhamnoides L.; dioecious; sex determination; RAPD; SCAR
Online: 9 April 2018 (10:48:47 CEST)
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The dioecious property of sea buckthorn (Hippophae rhamnoides L.) prevents sex recognition via traditional observation at the juvenile stage, thus impeding breeding and economic cropping; RAPD and SCAR markers were used to identify the sexes. A total of 45 random decamer primers were used to screen genomic DNA pools of staminate and pistillate genotypes for genetic polymorphisms. One female sex-linked marker was identified. D15 (5′-CATCCGTGCT-3′) amplified a particular band of 885 bp, which showed polymorphism among staminate and pistillate genotype plants. The SCAR marker Hrcx-15 was obtained by sequencing the fragment. The alleles of 140 pistillate genotypes were examined but not of the 140 staminate genotypes discerned via taxonomy. Staminate and pistillate genotypes of sea buckthorn plants can be distinguished, using Hrcx-15 as a genetic marker for sex identification and for expediting cultivation for commercial applications.
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Biology, Plant Sciences; Clematis; chloroplast genome; rearrangement; inversion; IR expansion; synonymous substitution rate
Online: 9 April 2018 (10:34:28 CEST)
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Genus Clematis is one of the largest within Ranunculaceae. Here we report the chloroplast genome of two Clematis species, C. brachyura and C. trichotoma endemic to Korea. The chloroplast genome lengths of C. brachyura and C. trichotoma are 159,532 bp and 159,170 bp, respectively. Gene contents in the complete chloroplast genomes of these two Clematis species are identical to that of most Ranunculaceae and other angiosperms. However, our data results demonstrated that genus Clematis has inversion and rearrangement events concerning gene rps4 gene, rps16 to trnH region, and trnL to ndhC region, and IR regions expansion. Comparison of IR regions among Ranunculaceae species revealed that Clematis species contained six protein coding genes (infA, rps8, rpl14, rpl16, rps3, and rpl22) usually found in the long single copy (LSC) region of other species. Phylogenetic analysis demonstrated that genus Clematis is closely related to genus Ranunculus. Differences in repeat structure, substitution rates, and IR expansion in genera Clematis and Ranunculus, explained their relationship. Clematis species showed slightly higher tandem repeats content than Ranunculus species. The six protein-coding genes showed lower synonymous substitution rates in the IR of Clematis species than in the LSC of Ranunculus species. Overall, the chloroplast genomes and results presented here provide important information on the evolution of Ranunculaceae.
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Biology, Plant Sciences; Idaeovirus; Blackcurrant leaf chlorosis associated virus; next-generation sequencing (NGS); bridge reads; abutting primers; RNase R digestion; circular RNA; concatenated RNA
Online: 30 March 2018 (11:40:46 CEST)
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Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and proposed as a new and distinct species in the genus Idaeovirus. Genomic components of BCLCaV that were detected and confirmed include: 1) RNA-1 that is monocistronic and encodes the replicase complex; 2) a bicistronic RNA-2 that encodes a movement protein (MP) and the coat protein (CP) of the virus, with open reading frames (ORF) that overlap by a single adenine (A) nucleotide (nt) representing the third position of an opal stop codon of the MP ORF2a and the first position of the start codon of the CP ORF2b; 3) a subgenomic form of RNA-2 (RNA-3) that contains ORF2b; and 4) a concatenated form of RNA-2 that consists of a complementary and inverted RNA-3 conjoined to the full-length RNA-2. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3’-terminus and 5’-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments with denaturation at 95 oC preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3.
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Biology, Plant Sciences; Keywords: TMV, plant vaccine, génital herpes, HSV-2, gD, VP16, GFP, mouse model genital herpes
Online: 28 March 2018 (09:18:30 CEST)
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A B S T R A C T Genital herpes disease is caused mainly by herpes simplex virus type 2 (HSV-2), which is sexually transmitted with a high prevalence in both developed and developing countries. No vaccine is currently available against genital herpes. In this study, we introduced and expressed two genes encoding HSV-2 glycoprotein D (gD) and VP16 protein and a GFP marker gene (control) in tobacco seedlings. Positive plant infection was assessed through characteristic tobacco mosaic virus disease symptoms on leaves and by monitoring the fluorescence emitted by the expressed GFP protein. Expression of the HSV-gD2 and VP16 antigens was verified by RT-PCR, ELISA and Western blot. As a proof of concept, the immunogenicity and the protection ability of the plant produced gD antigen was tested in a mouse model of genital herpes and compared to gD antigen produced in a mammalian expression system. This showed that the plant-gD preparation, when used in combination with a CpG oligodeoxynucleotide as adjuvant, was highly immunogenic and capable of inducing complete immunity to lethal vaginal HSV-2 challenge in mice. Thus, the data presented here may have implications for the development of a production system for highly immunogenic plant-based HSV-2 vaccine antigens.
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Biology, Plant Sciences; color tests; thin layer chromatography; chemotaxonomy; secondary metabolites; solvent system
Online: 24 February 2018 (08:28:11 CET)
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Presence and identity of secondary metabolites are two of the main components of lichen taxonomy. Aromatic compounds formed via the acetyl-polymalonate pathway are the most studied lichen substances. In addition, compounds derived from the mevalonic acid pathway (e.g., terpenes and steroids) are sometimes detected in the medulla. However, their identity and value as diagnostic characters in the genus Usnea are yet poorly understood despite the fact that they were mentioned in several taxonomical papers. We conclude that i) aside from the previously recognized polyphenolic compounds, carbohydrates and steroids are also detected in the medulla of some Usnea species; ii) the use of sulfuric anisaldehyde reagent greatly improves the detection of terpenes, carbohydrates and steroids compared with the sulfuric acid reagent routinely used in thin layer chromatography; iii) among carbohydrates, we detected arabitol and sucrose in the medulla; iv) steroids and terpenes remain unidentified and deserve further investigations.
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Sergei Kliver,
Mike Rayko,
Alexey Komissarov,
Evgeny Bakin,
Daria Zhernakova,
Kasavajhala V. S. K. Prasad,
Catherine Rushworth,
R. Baskar,
Dmitry Smetanin,
Jeremy Schmutz,
Daniel S. Rokhsar,
Thomas Mitchell-Olds,
Ueli Grossniklaus,
Vladimir Brukhin
Biology, Plant Sciences; Boechera; Brassicaceae; genome; assembly; annotation; apomixis
Online: 14 February 2018 (07:29:29 CET)
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Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of the apomictic species Boechera divaricarpa. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. 27048 protein-coding genes were predicted using a hybrid approach that combines homology-based and de novo methods. Also repeats, tRNA and rRNA genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. Also, a detailed analysis of evolution of the APOLLO apomixis-associated locus was performed. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species such as B. divaricarpa.
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Huili Yan,
Wenxiu Xu,
Jianyin Xie,
Yiwei Gao,
Lulu Wu,
Liang Sun,
Xu Chen,
Tian Zhang,
Changhua Dai,
Xiuni Lin,
Lu Feng,
Xueqiang Wang,
Fengmei Li,
Xiaoyang Zhu,
Jinjie Li,
Zichao Li,
Caiyan Chen,
Mi Ma,
Hongliang Zhang,
Zhenyan He
Biology, Plant Sciences; OsCd1; Cadmium accumulation; rice grain; indica; japonica; GWAS
Online: 9 February 2018 (07:13:17 CET)
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Cadmium accumulation in rice grain poses a serious threat to people’s health. Understanding the genetic basis on grain cadmium accumulation facilitates efforts to reduce it. Here, we show that OsCd1 is involved in Cd uptake and contributes to grain accumulation in rice. Natural variation in OsCd1 with a missense mutation Val449Asp is responsible for the divergence of rice grain cadmium accumulation between japonica and indica. Notably, near-isogenic line tests confirmed that the indica variety carrying the OsCd1V449 allele could reduce the grain cadmium accumulation. The favorable allele OsCd1V449 may be an important genetic resource to reduce grain cadmium accumulation for indica.
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Biology, Plant Sciences; protease; plant; pathogen; defence; substrate; immunity; hypersensitive response; recognition; signalling; priming
Online: 5 February 2018 (04:11:42 CET)
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Proteases are integral enzymes of the plant immune system. Multiple aspects of defence are regulated by proteases, including the hypersensitive response, pathogen recognition, priming and peptide hormone release. These processes are regulated by unrelated proteases residing at different subcellular locations. In this review we discuss ten prominent plant proteases contributing to the plant immune system, highlighting the diversity of roles they perform in plant defence.
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Biology, Plant Sciences; cold stress; heat stress; stress recovery; mitochondria; proteomics; respiration; Brassica; angiosperms
Online: 30 January 2018 (10:31:07 CET)
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Complex proteomic and physiological approaches to study cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by 2D PAGE in relation to respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold alternative oxidase isoforms were extensively upregulated; major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. On the contrary, distinct proteins, including carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Few metabolic regulations were suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse mode (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations on molecular and physiological levels. This implies more complex model of action of investigated stresses on plant mitochondria.
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Biology, Plant Sciences; dehydrins; 2D PAGE; drought; mitochondrial biogenesis; mitochondrial proteome; plant transcriptome
Online: 30 January 2018 (04:17:44 CET)
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The early generative phase of cauliflower (Brassica oleracea var. botrytis) curd ripening is sensitive to the water deficit. Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate the mitochondrial biogenesis of three cauliflower cultivars varying with drought tolerance. Diverse quantitative changes (down-regulations mostly) in the mitochondrial proteome were assayed by 2D PAGE coupled with LC-MS/MS. Respiratory (e.g. CII, CIV and ATP synthase subunits), transporter (including diverse porin isoforms) and matrix multifunctional proteins (e.g. components of RNA editing machinery) appeared diversely affected in their abundance under two drought levels. Western immunoassays showed also cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides found in few 2D spots that appeared immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The level of selected messengers participating in drought response was also determined. We conclude that the mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars and associated with drought tolerance on the proteomic and functional levels. However, transcriptomic and proteomic regulations were largely uncoordinated due to the suggested altered availability of messengers for translation, mRNA/ribosome interactions and/or miRNA impact on transcript abundance and translation.
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Biology, Plant Sciences; CO2; adaptation; photosynthesis; growth; weeds; carboxylation efficiency
Online: 22 January 2018 (17:44:14 CET)
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Seeds of three C3 and one C4 annual weedy species were collected from agricultural fields in Beltsville, Maryland in 1966 and 2006, when atmospheric CO2 concentrations averaged about 320 and 380 mmol mol-1, respectively. Plants from each collection year were grown over a range of CO2 concentrations to test for adaptation of these weedy species to recent changes in atmospheric CO2. In all three of the C3 species, the increase in CO2 concentration from 320 to 380 mmol mol-1 increased total dry mass at 24 days in plants from seeds collected in 2006, but not in plants from seeds collected in 1966. Shoot and seed dry mass at maturity was greater at the higher growth CO2 in plants collected in 2006 than in 1966 in two of the species. Down regulation of photosynthetic carboxylation capacity during growth at high CO2 was less in the newer seed lots than in the older in two of the species. Overall, the results indicate that adaptation to recent changes in atmospheric CO2 has occurred in some of these weedy species.
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Biology, Plant Sciences; somaclones; micropropagation; cactus; Cactaceae; microsatellite.
Online: 15 January 2018 (17:07:19 CET)
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Somaclones with typical and atypical shoots were regenerated from a callus culture in the same culture medium and in equal culture conditions. Since the genetic relationship among regenerated somaclones has not been investigated, current study employed heterologous microsatellite primers to examine the molecular diversity within and among somaclones, showing typical and atypical phenotypes with high morphological divergence. Nei identity value calculated between the somaclones was high (I = 0.929) and AMOVA showed higher genetic variation within (96%) than among (4%) the samples of somaclones. The polymorphism in the microsatellite loci indicated high levels of mean observed and expected heterozygosity in atypical somaclones, presumably with high adaptive potential and as source of genotypes for generation of new varieties of ornamental cacti. Low molecular divergence between typical and atypical morphologies of somaclones is a promising perspective for use of the atypical somaclones as source of chemical compounds of commercial and industrial interest. The somaclonal variations occurring in vitro callus culture has generated phenotypically differentiated subpopulations with low molecular divergence, however with high genetic variability, enough to be recommended as a source of genotypes to generate new varieties of ornamental cacti and of plants with new traits, necessary for breeding programs.
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Biology, Plant Sciences; Actinidia deliciosa; ethylene; fruit ripening; mass spectrometry; post-harvest; proteomics
Online: 29 December 2017 (09:01:57 CET)
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An understanding of the mechanism underlying fruit ripening is critical for fruit quality improvement. Although post-harvest ethylene application is known to enhance the onset of fruit ripening, exact mechanisms remain unclear. To characterize the fruit ripening process and mechanism, we investigated the effects of exposing kiwifruit cultivars ‘Hayward’ and ‘Gamrok’ to exogenous ethylene treatment post-harvest using comprehensive proteomic analyses. Comparative two-dimensional gel electrophoresis showed that most of the proteins aggregated in ethylene-treated samples compared to the control (non-treated). We observed that among all ethylene treatments, 95 proteins from ‘Hayward’ and 106 from ‘Gamrok’ were differentially expressed. Interestingly, among the elicited protein successfully identified by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry, 50% from “Hayward’ and 60% from ‘Gamrok’ are associated with fruit ripening. Furthermore, 18% and 10% of proteins, respectively, are associated with defense response, whereas other major proteins are related to protein biosynthesis and photosynthesis/Calvin cycle. Interactions between identified proteins were demonstrated by bioinformatic analysis, providing insights into biological pathways and molecular functions in post-harvest kiwifruit ripening elicited by ethylene application. The present proteomic study in accordance with physiological analysis provides a quantitative evaluation of fruit ripening in response to exogenous ethylene in post-harvest kiwifruit.
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Biology, Plant Sciences; pre-harvest; ripeness; image analysis; machine learning; fruit phenotyping
Online: 20 December 2017 (09:35:36 CET)
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Global food security for the increasing world population not only requires increased sustainable production of food but a significant reduction in pre- and post-harvest waste. The timing of when a fruit is harvested is critical for reducing waste along the supply chain and increasing fruit quality for consumers. The early in field assessment of fruit ripeness and prediction of the harvest date and yield by non-destructive technologies have the potential to revolutionize farming practices and enable the consumer to eat the tastiest and freshest fruit possible. A variety of non-destructive techniques have been applied to estimate the ripeness or maturity but not all of them are applicable for in situ (field or glasshouse) assessment. This review focuses on the non-destructive methods which are promising, or have already been, applied to the pre-harvest in field measurement including colorimetry, visible imaging, spectroscopy and spectroscopic imaging. Machine learning and regression models used in assessing ripeness are also discussed.
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Mehdi Sharifi-Rad,
Elena Maria Varoni,
Bahare Salehi,
Javad Sharifi-Rad,
Karl R. Matthews,
Seyed Abdulmajid Ayatollahi,
Farzad Kobarfard,
Salam A. Ibrahim,
Dima Mnayer,
Zainul Amiruddin Zakaria,
Majid Sharifi-Rad,
Zubaida Yousaf,
Marcello Iriti,
Adriana Basile,
Daniela Rigano
Biology, Plant Sciences; Zingiber; ginger; essential oil; rhizome; herbal remedies; traditional healing systems; food preservatives
Online: 16 November 2017 (04:38:52 CET)
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Plants of the genus Zingiber (Family Zingiberaceae) are widely used throughout the world as food and medicinal plants. They represent very popular herbal remedies in various traditional healing systems; in particular, rhizome of Zingiber spp. plants has a long history of ethnobotanical uses because of a plethora of curative properties. Antimicrobial activity of rhizome essential oil has been extensively confirmed in vitro and attributed to its chemical components, mainly consisting in monoterpene and sesquiterpene hydrocarbons such as α-zingiberene, ar-curcumene, β-bisabolene and β-sesquiphellandrene. In addition, gingerols have been identified as the major active components in the fresh rhizome, whereas shogaols, dehydrated gingerol derivatives, are the predominant pungent constituents in dried rhizome. Zingiber spp. may thus represent a promising and innovative source of natural alternatives to chemical food preservatives. This approach would meet the increasing concern of consumers aware of the potential health risks associated with the conventional antimicrobial agents in food. This narrative review aims providing a literature overview on Zingiber spp. plants, their cultivation, traditional uses, phytochemical constituents and biological activities.
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Biology, Plant Sciences; RGSV; movement proteins; gene silencing; transgenic mechanism; virus-induced small interfering RNA; RNA silencing pathway; antiviral plant defenses
Online: 2 November 2017 (03:05:04 CET)
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Rice grassy stunt virus (RGSV) a member of Tenuivirus family, is very potent and destructive which effects rice crop in many countries, particularly China. Non coding RNAs have important functions in development and epigenetic regulation of gene expression in numerous organsisms. There is three type of small non coding RNAs have been found in eukaryotes, which are small interferring RNAs (siRNAs), microRNAs (miRNAs) and piwi interacting RNAs (piRNAs). Small RNAs (sRNAs) origination is from the infecting virus which is known as virus-derived small interfering RNAs (vsiRNAs), has responsibility for RNA silencing in plants. Virus-induced gene silencing (VIGS) is mainly dependent on RNA silencing (RNAi). Interestingly, RNA silencing happens in plants during viral infections. RNAi technique showed significant results in Nephotettix cincticeps. RNAi technique demonstrated the gene silencing of planthopper Nilaparvata lugens. The proteins P5, pcf4, Dnj, psn5, and pn6 act as potential movement proteins and serve as silencing suppressors for RGSV. VsiRNAs originate from dsRNA molecules which require Dicer-like (DCL) proteins, RNA dependent RNA polymerase (RdRP) proteins, and Argonaute (AGO) proteins. RdRP uses ssRNA for perfect RNA amplification process and can also be used for DCL dependent secondary vsiRNA formation. VSRs interfere with the movement of signals during silencing mechanism. Moreover, intercellular movement of viruses is facilitated by virus-encoded movement protein. RNAi is found in many eukaryotes which are related to transcriptional or post-transcriptional regulation by gene suppression. Transcription is bidirectional in ssDNA viruses which are originated from dsRNA molecules. In this review, we highlighted the biology of Rice grassy stunt virus and its insect vector and its silencing suppressors. This work will be helpful for plant virologists to understand the whole biogenesis mechanism for rice viruses especially RGSV.
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Biology, Plant Sciences; common bean; soybean; Argonaute5; legume-rhizobia symbiosis
Online: 18 October 2017 (03:20:37 CEST)
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The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, is able to bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 hour of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: NUCLEAR FACTOR Y-B (NF-YB), NODULE INCEPTION (NIN) and FLOTILIN2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia in determinate legumes.
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Biology, Plant Sciences; arsenic pollution; differential display; genes; resistance; rice crop; soil contamination
Online: 22 June 2017 (05:16:08 CEST)
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The main objective of the present study was to investigate arsenate [As (V)] resistance genes in rice cultivars grown in arsenic contaminated Egyptian soil in order to genetically induce resistance against arsenic in the local rice varieties as well as defining contaminated rice grains and/or soil. Three local rice cultivars; Sakha 102-104 were cultivated on modified Murashige and Skoog Basal Medium (MS medium) containing elevated concentrations of arsenate (0.1, 1 and 10 mg/l). The three varieties showed different resistant attitudes against arsenate with Sakha 104 being the most resistant. Extracted messenger RNA (mRNA) from treated and untreated Sakha 104 plantlets was scanned using differential display to demonstrate the arsenate resistant genes using three different arbitrary primers. About 100 different RNAs with (1500 bp - 50 bp) were obtained from which seven were up-regulated genes, subjected to DNA cloning using TOPO TA system and the selected clones were sequenced. The sequence analysis described four genes out of the seven namely disease resistance protein RPM1, Epstein-Barr virus EBNA-1-like, CwfJ family protein and outer membrane lipoprotein OmlA while the other three genes were hypothetical proteins. It is concluded the four induced genes in the resistant rice cultivar considered as a direct response to arsenic soil pollution. Genes detected in the present study can be used as geno-sensors for rice grains and soil contamination with As (V). Moreover, local rice cultivars may be genetically modified with such genes to induce high resistance and to overcome arsenic soil pollution.
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Biology, Plant Sciences; Pittosporum tobira (Thunb.) Aiton; Essential oils (EOs); Headspace solid-phase microextraction (HS-SPME); Gas chromatography-mass spectrometry (GC-MS); Anticancer activity
Online: 17 May 2017 (13:08:12 CEST)
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Background: Pittosporum tobira (Thunb.) Aiton is an aromatic medicinal plant widely cultivated in the world. However, the essential oils (EOs) from P. tobira flowers for anti-cancer potential is still not systematically studied. The present aim to elucidate the phytochemical composition of the EOs and to explore mechanism of anticancer action. Methods: The EOs were extracted and analyzed by headspace solid-phase microextraction (HS-SPME) with gas chromatography-mass spectrometry (GC-MS). Volatile components were identified according to Kovats retention index (KI) and NIST database. The anti-neoplasm mechanisms of the EOs was comprehensively investigated in lung carcinoma A549 and H460 cells. Results: A total of 47 secondary metabolites representing 94.18% of the EOs were successfully identified: monoterpenes and sesquiterpenes were the dominant terpenoids. The EOs exhibited antiproliferative activity on A549 and H460 lung carcinoma cells. Hoechst 33324 fluorescent staining indicated the typical characteristics of apoptosis and induced cycle phase arrest. AnnexinV/PI staining revealed that the number of apoptotic cells was increased. Furthermore, the EOs also induced the caspase-mediated mitochondrial apoptosis pathway. Conclusions: Findings suggest that the full-scale chemical composition and first characterization of anticancer activities of the EOs, it could be used for integrative natural anti-cancer agents in health care should be pay more attention.
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Biology, Plant Sciences; Turnip mosaic virus; Potyvirus; Genetic structure; Population; China
Online: 15 May 2017 (11:38:11 CEST)
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Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis. To understand the genetic structure of TuMV from radish in China, the 3′-terminal genome of 90 TuMV isolates were determined and analyzed with other Chinese isolates available. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai’an, Weifang and Changchun was frequent.
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Biology, Plant Sciences; Chromatin and transcription dynamics; reproductive development; differentiation; ChIP-seq; RNA-seq
Online: 8 May 2017 (18:25:10 CEST)
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Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes, respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related H3K4me3. However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with transcriptional changes, in a developmental series including Arabidopsis leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prime over changes in H3K27me3 and quantitatively correlate with transcription changes, while H3K27me3 changes occur after prolonged expression changes. Notably, early activation of PcG target genes is dominated by increases in H3K4me3 while H3K27me3 remains present at the locus. Our results reveal H3K4me3 as greater predictor over H3K27me3 for transcription dynamics, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.
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Biology, Plant Sciences; Parmelina; phenols; HPLC; myeloconone C
Online: 30 March 2017 (16:58:33 CEST)
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We cultured Parmelina carporrhizans and P. quercina in Corn Meal Agar and 0.2% glucose Malt Yeast Agar for 160 days. Chemosyndrome of natural thalli and mycobiont cultures were analyzed by HPLC. Lecanoric acid, atranorin, chloratranorin and ergosterol were detected in P. carporrhizans thalli, while lecanoric acid, chloratranorin and aliphates were found in P. quercina thalli. The secondary methabolites pattern between thalli and mycobiont culture was completely different in both species. Both species secreted the phenalenone myeloconone C in culture media and was also detected in P. quercina mycobiont aggregates. Interestingly, the phenolic compounds produced by the mycobiont culture of P. carporrhizans are related to those produced by natural thallus by the same biosynthetic pathway, while the chemosyndrome of P. quercina mycobiont implies switch of biosynthetic pathway from acetate-polymalonate pathway to shikimic acid pathway, with pulvinic acid as major compound of mycobiont culture. The role of Myelochonone C, confluentic acid and pulvinic acid produced by mycobiont culture is discussed as possible adaptive vantage in field as photoprotective agent or as byproduct result of stressing artificial culture conditions.
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Biology, Plant Sciences; Fritillaria ussuriensis, Fritillaria cirrhosa, Chloroplast genome, Comparative analysis, Highly divergent region
Online: 17 March 2017 (16:30:34 CET)
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The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 protein-coding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species’ cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.
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Biology, Plant Sciences; Rhododendron chrysanthum Pall.; cold stress; chlorophyll fluorescence; photosynthesis; antioxidant enzymes
Online: 17 March 2017 (04:46:21 CET)
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Rhododendron chrysanthum Pall., live in Changbai Mountain being exposed to chilling temperature, high light intensities and water scarcity condition. To adapt to the harsh environment, the cold resistance mechanisms of R. chrysanthum have been successfully evolved in the long-term adaptive process. In our present work, the methods of proteomics combined with physiological and biochemical analyses were used to investigate the effects of cold stress on the photosynthesis and antioxidant system of Rhododendron chrysanthum Pall. and the molecular mechanisms involved in cold resistance of plants. A total of 153 photosynthesis related proteins were identified in present work, of which 7 proteins including Rubisco large subunit (rbcL) were up-regulated in experiment group (EG) compared with control group (CG). Simultaneously, four chlorophyll fluorescence parameters were measured in present study. The results showed that the maximum photochemical efficiency of photosystem II (Fv/Fm), actual quantum yield of PSII (Y(II)) and photochemical quenching (qP) were significantly higher in EG, whereas the non-photochemical quenching (NPQ) was notably decreased. Cold stress could lead to a significant reduction in electron transport rate (ETR) accompanied with an increase in excitation pressure (1-qP). The abundance of PetE which involved in the plants photosynthetic electron transfer was also significantly influenced by cold stress. Moreover, the up-regulated expressions and higher levels of enzymatic activities of Glutathione peroxidase (GPX) and Ascorbate peroxidases (APXs) were detected in EG. All these changes which can help plants to survive in low temperature are considered as the crucial parts of cold tolerance mechanisms. These results revealed that photosynthesis and redox adjustment play significant roles in the defense of cold-induced damage.
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Biology, Plant Sciences; Adaptive mechanisms; antioxidative metabolism; chloroplast; osmotic regulation; oxidative stress; photosynthesis; salinity; water relations
Online: 24 February 2017 (10:21:50 CET)
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This review deals with the adaptive mechanisms that plants can implement to cope with the challenge of salt stress. Plants tolerant to NaCl implement a series of adaptations to acclimate to salinity, including morphological, physiological and biochemical changes. These changes include increases in the root/canopy ratio and in the chlorophyll content in addition to changes in the leaf anatomy that ultimately lead to preventing leaf ion toxicity, thus maintaining the water status in order to limit water loss and protect the photosynthesis process. Furthermore, we deal with the effect of salt stress on photosynthesis and chlorophyll fluorescence and some of the mechanisms thought to protect the photosynthetic machinery, including the xanthophyll cycle, photorespiration pathway and water-water cycle. Finally, we also provide an updated discussion on salt-induced oxidative stress at the subcellular level and its effect on the antioxidant machinery in both salt-tolerant and salt-sensitive plants. The aim is to extend our understanding of how salinity may affect the physiological characteristics of plants.
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Biology, Plant Sciences; ecosystem services; urban water; Warsaw; Poland; environment
Online: 13 February 2017 (09:30:21 CET)
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Urban lakes, especially those of natural origin, provide ecosystem services, recreation being one of the most important and highly valued by the city dwellers. Fulfilling the needs of city residents to relax and have contact with nature has become a priority in urbanized areas and has been proved to positively affect people’s health and well-being. The recreational potential of water bodies was identified to be most important aspect of ecosystem services to the residents of the neighboring areas. An assessment of recreational ecosystem services (RES) provisioning to society based on the real time spent by the citizens and housing values in the rural-urban gradient revealed that the economic benefits of lakes differ in urbanized, suburban and rural landscapes. The growth of cities has led to an increased population density in the surroundings of ecologically valuable areas, resulting in higher pressure from visitors seeking recreational areas. Along with urbanization, the impoverishment of ecosystem functions takes place, limiting their capability to provide ecosystem services. In this work provisioning of recreational ecosystem services of 28 floodplain lakes located along the urban-rural gradient of the Warsaw agglomeration was assessed. The relationship between the ecological value of the water bodies, measured using naturalness indices, and the recreational ecosystem services they can provide was assessed. The results showed that the floodplain lakes located along the urban-rural gradient are of a great importance to the citizens due to their recreational potential. The provisioning of recreational ecosystem services is poorly connected with the ecological characteristics of the floodplain lakes. Only hemeroby, was significantly correlated with provisioning, and there was no relationship with factors such as naturalness of vegetation or water quality, demonstrating that public preference was not generally influenced by high ecological quality. These data should be available to potential buyers and be integrated in spatial planning management plans in order to shape future housing policy.
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Biology, Plant Sciences; Acer truncatum leaves; ultrasonic-assisted extraction; response surface methodology; phenolics; antioxidant activity; UPLC-QTOF-MS/MS
Online: 9 January 2017 (04:16:01 CET)
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This study was designed for the first time to improve phenolic yield and antioxidant activity of ultrasonic-assisted extraction from Acer truncatum leaves (ATL) using response surface methodology, and phenolic composition in ATL extracted under the optimized condition were characterized by UPLC-QTOF-MS/MS. Solvent and extraction time were selected based on preliminary experiments, and a four-factors-three-levels central composite design was conducted to optimize solvent concentration (X1), material-to-liquid ratio (X2), ultrasonic temperature (X3) and power (X4) for an optimal total phenol yield (Y1) and DPPH• antioxidant activity (Y2). The results showed that the optimal combination was ethanol: water (v:v) 66.21%, material-to-liquid ratio 1:15.31 g/mL, ultrasonic temperature 60 °C, power 267.30 W, and time 30 min with three extractions, giving a maximal total phenol yield of 7593.62 mg gallic acid equivalent /100 g d.w. and a maximal DPPH• antioxidant activity of 74241.61 μmol Trolox equivalent/100 g d.w.. Furthermore, 22 phenolics were first identified in ATL extract obtained under the optimized conditions, indicating that gallates, gallotannins, quercetin, myricetin and chlorogenic acid derivatives were the main phenolic composition in ATL. What’s more, a gallotannins pathway existing in ATL from gallic acid to penta-O-galloyl-glucoside was interpreted. All these results provided practical information aiming at full utilization of phenolics in ATL, together with fundamental knowledge for further research.
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Biology, Plant Sciences; AmRosea1 gene; transcriptome analysis; drought tolerance; salt tolerance; rice
Online: 14 December 2016 (09:16:50 CET)
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Ectopic expression of the MYB transcription factor of AmROSEA1 from Antirrhinum majus has been reported to change anthocyanin and other metabolites in several species. In this study, we found that overexpression of AmRosea1 significantly improved the tolerance of transgenic rice to drought and salinity stress. Transcriptome analysis revealed that a considerable amount of stress-related genes were affected by exogenous AmRosea1 during both drought and salinity stress treatments. These affected genes are involved in stress signal transduction, the hormone signal pathway, ion homeostasis and the enzymes that remove peroxides. This work suggests that the AmRosea1 gene is a potential candidate for genetic engineering of crops.
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Biology, Plant Sciences; calcium; protons; exocytosis; tip growth; Lilium; pollen; respiration; perturbation analysis
Online: 1 November 2016 (05:25:42 CET)
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Pollen tubes grow by spatially and temporally regulated expansion of new material secreted into the cell wall at the tip of the tube. A complex web of interactions among cellular components, ions and small molecule provides dynamic control of localized expansion and secretion. Cross-correlation studies on oscillating lily (Lilium formosanum Wallace) pollen tubes showed that an increase in intracellular calcium follows an increase in growth, whereas the increase in the alkaline band and in secretion both anticipate the increase in growth rate. Calcium, as a follower, is unlikely to be a stimulator of growth, whereas the alkaline band, as a leader, may be an activator. To gain further insight herein we reversibly inhibited growth with potassium cyanide (KCN), and followed the re-establishment of calcium, pH and secretion patterns as growth resumed. While KCN markedly slows growth and causes the associated gradients of calcium and pH to sharply decline, its removal allows growth and vital processes to fully recover. The calcium gradient reappears before growth restarts, however it is preceded by both the alkaline band and secretion, in which the alkaline band is slightly advanced over secretion. Thus the pH gradient, rather than the tip-focused calcium gradient, may regulate pollen tube growth.
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Biology, Plant Sciences; EST-SSR marker; hexaploid; sweet potato; polymorphic; sequence
Online: 20 September 2016 (11:35:51 CEST)
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According to statistics from the Food and Agriculture Organization, the world population will increase to about 91 million (Asia 51 million, Africa 19 million). A rise in the world’s population means an increased need for food. However, climate change has caused desertification and unpredictable weather, creating problems in the supply and demand of food. Sweet potato (Ipomoea batatas) is an alternative to solving the food problem, as it is one of the world’s most important food crops, especially in developing countries. The tuberous roots of sweet potato are usually used as staple food, animal feed, industrial material, or raw material for alcohol production. In the future, more variations of sweet potato will be needed for breeding this crop. Recently, molecular markers developed for sweet potato have demonstrated good potential for use in genetic selection. In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag–simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.
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Biology, Plant Sciences; Nicotiana tabacum; solanesol; RNA-seq; solanesyl diphosphate synthase; gene expression; chlorophyll
Online: 18 September 2016 (10:45:27 CEST)
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Solanesol is a noncyclic terpene alcohol composed of nine isoprene units and it mainly accumulates in solanaceous plants, especially tobacco (Nicotiana tabacum L.). Here, RNA-seq analyses of tobacco leaves, stems, and roots were used to identify solanesol biosynthesis genes. Six 1-deoxy-d-xylulose 5-phosphate synthase, two 1-deoxy-d-xylulose 5-phosphate reductoisomerase, two 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase, four 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase, two 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase, four 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, two 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, six isopentenyl diphosphate isomerase, and two solanesyl diphosphate synthase (SPS) genes were identified to be involved in solanesol biosynthesis. Furthermore, the two N. tabacum SPS (NtSPS1 and NtSPS2), which had two conserved aspartate-rich DDxxD domains, were highly homologous with SPS enzymes from other solanaceous plant species. In addition, the solanesol contents of three organs, and leaves from four growing stages, corresponded with the distribution of chlorophyll. Our findings provide a comprehensive evaluation of the correlation between the expression of different biosynthetic genes and the accumulation of solanesol in tobacco.
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Biology, Plant Sciences; oligopeptide transporters (OPTs); Medicago truncatula; phylogenetic analysis; gene express
Online: 15 September 2016 (08:39:23 CEST)
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Oligopeptide transporters (OPTs) are a group of membrane localized proteins that have a broad range of substrate transport capabilities and contribute to numerous biological processes. However, limited information has been reported on OPTs in higher plants. In this study, a comprehensive analysis of the OPT gene family in Medicago truncatula was performed. A total of 26 OPT genes (MtOPT01-MtOPT26) have been identified in the Medicago truncatula genome. Phylogenetic analyses indicated that MtOPTs consisted of two distinct subgroups, 12 MtOPTs belonged to the peptide transport subgroup (PT-OPT) based on their predicted amino acid sequences containing the two highly conserved motifs (NPG and KIPPR) and 14 MtOPTs belonged to yellow stripe subgroup (YS-OPT). The MtOPTs distributed on each of 8 chromosomes in Medicago truncatula. Sequence analysis verified that MtOPTs significant similar to those in other plants. The copy number of MtOPTs was low and the multiply of MtOPTs was simple relatively. Gene structure analysis showed that most of the MtOPTs have various numbers of introns. The multiple of MtOPTs might play different biological roles which were supported by the fact that MtOPTs have a distinct tissue-specific expression pattern. The data obtained in this study will help to better understand the complexity of the MtOPTs gene family and provide new evidence for the function and evolution of the OPT gene family in higher plants.
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Biology, Plant Sciences; Consolida orientalis; ethyl acetate extract; antioxidant activity; β-sitosterol
Online: 9 September 2016 (11:18:02 CEST)
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General phytochemical screening of the aerial parts of Consolida orientalis revealed the presence of steroids, terpenes, phenolic compounds, saponins, fatty acids, alkaloids. This study was conducted to investigate the bioactivities of extracts, isolation and identification the compounds from aerial parts of C.orientalis. The main goal of the present study is identifying and characterizing the antioxidant activity of the Consolida orientalis and biological isolation of active terpenoid. Aerial parts of the plant were dried at room temperature and reduced to small pieces, followed by using extraction with ethyl acetate percolation. Tree complementary analysis system was used, DPPH free radical scavenging test, total phenolic metabolites and FRAP. The total phenolic content was 38.83±2.09 mg gallic acid corresponding to g-1 extract with regarding to standard curve (y=0.0054x+0.0488, r2=0.995). IC50 value for DPPH radical – scavenging was 987.11±28.66 mgml-1. The extract was exhibited a medium reducing power compared with Vit C. The isolation and purification was afforded white crystalline powder which was subjected to physical, chemical and spectral identification by IR, 1H- and 13C- NMR and GC-MS. Isolated compound was identified as β-sitosterol. That is a terpenoid with melting point 133.4-134.5 ͦ c and with molecular formula C29H50O.