ResearchPad - plant-science https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis]]> https://www.researchpad.co/article/elastic_article_13837 In single-cell RNA-seq (scRNA-seq) experiments, the number of individual cells has increased exponentially, and the sequencing depth of each cell has decreased significantly. As a result, analyzing scRNA-seq data requires extensive considerations of program efficiency and method selection. In order to reduce the complexity of scRNA-seq data analysis, we present scedar, a scalable Python package for scRNA-seq exploratory data analysis. The package provides a convenient and reliable interface for performing visualization, imputation of gene dropouts, detection of rare transcriptomic profiles, and clustering on large-scale scRNA-seq datasets. The analytical methods are efficient, and they also do not assume that the data follow certain statistical distributions. The package is extensible and modular, which would facilitate the further development of functionalities for future requirements with the open-source development community. The scedar package is distributed under the terms of the MIT license at https://pypi.org/project/scedar.

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<![CDATA[Genome reconstruction of the non-culturable spinach downy mildew <i>Peronospora effusa</i> by metagenome filtering]]> https://www.researchpad.co/article/elastic_article_13800 Peronospora effusa (previously known as P. farinosa f. sp. spinaciae, and here referred to as Pfs) is an obligate biotrophic oomycete that causes downy mildew on spinach (Spinacia oleracea). To combat this destructive many disease resistant cultivars have been bred and used. However, new Pfs races rapidly break the employed resistance genes. To get insight into the gene repertoire of Pfs and identify infection-related genes, the genome of the first reference race, Pfs1, was sequenced, assembled, and annotated. Due to the obligate biotrophic nature of this pathogen, material for DNA isolation can only be collected from infected spinach leaves that, however, also contain many other microorganisms. The obtained sequences can, therefore, be considered a metagenome. To filter and obtain Pfs sequences we utilized the CAT tool to taxonomically annotate ORFs residing on long sequences of a genome pre-assembly. This study is the first to show that CAT filtering performs well on eukaryotic contigs. Based on the taxonomy, determined on multiple ORFs, contaminating long sequences and corresponding reads were removed from the metagenome. Filtered reads were re-assembled to provide a clean and improved Pfs genome sequence of 32.4 Mbp consisting of 8,635 scaffolds. Transcript sequencing of a range of infection time points aided the prediction of a total of 13,277 gene models, including 99 RxLR(-like) effector, and 14 putative Crinkler genes. Comparative analysis identified common features in the predicted secretomes of different obligate biotrophic oomycetes, regardless of their phylogenetic distance. Their secretomes are generally smaller, compared to hemi-biotrophic and necrotrophic oomycete species. We observe a reduction in proteins involved in cell wall degradation, in Nep1-like proteins (NLPs), proteins with PAN/apple domains, and host translocated effectors. The genome of Pfs1 will be instrumental in studying downy mildew virulence and for understanding the molecular adaptations by which new isolates break spinach resistance.

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<![CDATA[Peach PpSnRK1 Participates in Sucrose-Mediated Root Growth Through Auxin Signaling]]> https://www.researchpad.co/article/elastic_article_13111 Sugar signals play a key role in root growth and development. SnRK1, as one of the energy centers, can respond to energy changes in plants and affect the growth and development of plants. However, studies on sugar signals and SnRK1 regulating root growth in fruit trees have not been reported. In this study, we found that 5% exogenous sucrose could increase the total volume and total surface area of the peach root system, enhance the number and growth of lateral roots, and promote the activity of SnRK1. When exogenous trehalose was applied, the growth of roots was poor. Sucrose treatment reversed the inhibitory effects of trehalose on SnRK1 enzyme activity and root growth. We also found that the lateral root number of PpSnRK1a-overexpressing plants (4-1, 4-2, and 4-3) increased significantly. Therefore, we believe that peach SnRK1 is involved in sucrose-mediated root growth and development. To further clarify this mechanism, we used qRT-PCR analysis to show that exogenous sucrose could promote the expression of auxin-related genes in roots, thereby leading to the accumulation of auxin in the root system. In addition, the genes related to auxin synthesis and auxin transport in the root systems of PpSnRK1a-overexpressing lines were also significantly up-regulated. Using peach PpSnRK1a as the bait, we obtained two positive clones, PpIAA12 and PpPIN-LIKES6, which play key roles in auxin signaling. The interactions between peach PpSnRK1a and PpIAA12/PpPIN-LIKES6 were verified by yeast two-hybrid assays and bimolecular fluorescence complementation experiments, and the complexes were localized in the nucleus. After exogenous trehalose treatment, the expression of these two genes in peach root system was inhibited, whereas sucrose had a significant stimulatory effect and could alleviate the inhibition of these two genes by trehalose, which was consistent with the trend of sucrose’s regulation of SnRK1 activity. In conclusion, peach SnRK1 can respond to sucrose and regulate root growth through the auxin signal pathway. This experiment increases our understanding of the function of fruit tree SnRK1 and provides a new insight to further study sugar hormone crosstalk in the future.

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<![CDATA[Effects of Light on Secondary Metabolites in Selected Leafy Greens: A Review]]> https://www.researchpad.co/article/elastic_article_13052 In contrast to the primary metabolism, responsible for essential synthesis mechanisms and mass balance in plants, the secondary metabolism is not of particular importance for each cell but for the plant organism as its whole. Most of these metabolites show antioxidant properties and are beneficial for human health. In order to affect accumulation of those metabolites, light is an essential factor. It is possible to select various combinations of light intensity and light quality to address corresponding photoreceptors and synthesis. However, the plethora of additional variables considering environmental conditions such as temperature, relative humidity or cultivation method complicate defining specific “light recipes”. This review summarizes experiments dealing with consumable leafy greens such as lettuce or basil and the enhancement of three selected metabolites – anthocyanins, carotenoids and flavonols.

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<![CDATA[Genetic Control of Reproductive Traits in Tomatoes Under High Temperature]]> https://www.researchpad.co/article/elastic_article_12995 Global climate change is increasing the range of temperatures that crop plants must face during their life cycle, giving negative effects to yields. In this changing scenario, understanding the genetic control of plant responses to a range of increasing temperature conditions is a prerequisite to developing cultivars with increased resilience. The current work reports the identification of Quantitative Trait Loci (QTL) involved in reproductive traits affected by temperature, such as the flower number (FLN) and fruit number (FRN) per truss and percentage of fruit set (FRS), stigma exsertion (SE), pollen viability (PV) and the incidence of the physiological disorder tipburn (TB). These traits were investigated in 168 Recombinant Inbred Lines (RIL) and 52 Introgression Lines (IL) derived from the cross between Solanum lycopersicum var. “MoneyMaker” and S. pimpinellifolium accession TO-937. Mapping populations were cultivated under increased temperature regimen conditions: T1 (25°C day/21°C night), T2 (30°C day/25°C night) and T3 (35°C day/30°C night). The increase in temperature drastically affected several reproductive traits, for example, FRS in Moneymaker was reduced between 75 and 87% at T2 and T3 when compared to T1, while several RILs showed a reduction of less than 50%. QTL analysis allowed the identification of genomic regions affecting these traits at different temperatures regimens. A total of 22 QTLs involved in reproductive traits at different temperatures were identified by multi-environmental QTL analysis and eight involved in pollen viability traits. Most QTLs were temperature specific, except QTLs on chromosomes 1, 2, 4, 6, and 12. Moreover, a QTL located in chromosome 7 was identified for low incidence of TP in the RIL population, which was confirmed in ILs with introgressions on chromosome 7. Furthermore, ILs with introgressions in chromosomes 1 and 12 had good FRN and FRS in T3 in replicated trials. These results represent a catalog of QTLs and pre-breeding materials that could be used as the starting point for deciphering the genetic control of the genetic response of reproductive traits at different temperatures and paving the road for developing new cultivars adapted to climate change.

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<![CDATA[A Trichome-Specific, Plastid-Localized <i>Tanacetum cinerariifolium</i> Nudix Protein Hydrolyzes the Natural Pyrethrin Pesticide Biosynthetic Intermediate <i>trans</i>-Chrysanthemyl Diphosphate]]> https://www.researchpad.co/article/elastic_article_12951 Tanacetum cinerariifolium flowers synthesize six pyrethrins that function as effective insecticides. trans-Chrysanthemol is an early intermediate in the synthesis of the monoterpene moiety of pyrethrins. Previously, the pyrethrum enzyme chrysanthemyl diphosphate synthase (TcCDS) was shown to catalyze the formation of the prenyl diphosphate compound chrysanthemyl diphosphate (CPP) by condensing two molecules of dimethylallyl diphosphate (DMAPP). Later work also showed that with a low concentration of DMAPP, TcCDS can also remove the diphosphate group to give chrysanthemol. The removal of the phosphate groups from other prenyl diphosphates, such as DMAPP, isopentenyl diphosphate (IPP) and geranyl diphosphate (GPP), was previously shown to occur in two steps. In those cases, the first phosphate group is removed by a member of the Nudix hydrolase protein family, and the second by other unidentified phosphatases. These previously characterized Nudix proteins involved in the hydrolysis of prenyl diphosphates were shown to be cytosolic. Here we report that a plastidic Nudix protein from pyrethrum, designated TcNudix1, has high specificity for CPP and can hydrolyze it to chrysanthemol monophosphate (CMP). TcNudix1 is expressed specifically in the trichomes of the ovaries, where chrysanthemol is produced. TcNudix1 expression patterns and pathway reconstitution experiments presented here implicate the TcNudix1 protein in the biosynthesis of chrysanthemol.

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<![CDATA[Early Evidence of Shifts in Alpine Summit Vegetation: A Case Study From Kashmir Himalaya]]> https://www.researchpad.co/article/elastic_article_12905 Under the contemporary climate change, the Himalaya is reported to be warming at a much higher rate than the global average. However, little is known about the alpine vegetation responses to recent climate change in the rapidly warming Himalaya. Here we studied vegetation dynamics on alpine summits in Kashmir Himalaya in relation to in situ measured microclimate. The summits, representing an elevation gradient from treeline to nival zone (3530–3740 m), were first surveyed in 2014 and then re-surveyed in 2018. The initial survey showed that the species richness, vegetation cover and soil temperature decreased with increasing elevation. Species richness and soil temperature differed significantly among slopes, with east and south slopes showing higher values than north and west slopes. The re-survey showed that species richness increased on the lower three summits but decreased on the highest summit (nival zone) and also revealed a substantial increase in the cover of dominant shrubs, graminoids, and forbs. The nestedness-resultant dissimilarity, rather than species turnover, contributed more to the magnitude of β-diversity among the summits. High temporal species turnover was found on south and east aspects, while high nestedness was recorded along north and west aspects. Thermophilization was more pronounced on the lower two summits and along the northern aspects. Our study provides crucial scientific data on climate change impacts on the alpine vegetation of Kashmir Himalaya. This information will fill global knowledge gaps from the developing world.

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<![CDATA[Post-transcriptional regulation of several biological processes involved in latex production in <i>Hevea brasiliensis</i>]]> https://www.researchpad.co/article/elastic_article_12852 Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea.MethodsGenes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators.ResultsCompared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers. ]]> <![CDATA[Reassessing the observational evidence for nitrogen deposition impacts in acid grassland: spatial Bayesian linear models indicate small and ambiguous effects on species richness]]> https://www.researchpad.co/article/elastic_article_12822 Nitrogen deposition (Ndep) is considered a significant threat to plant diversity in grassland ecosystems around the world. The evidence supporting this conclusion comes from both observational and experimental research, with “space-for-time” substitution surveys of pollutant gradients a significant portion of the former. However, estimates of regression coefficients for Ndep impacts on species richness, derived with a focus on causal inference, are hard to locate in the observational literature. Some influential observational studies have presented estimates from univariate models, overlooking the effects of omitted variable bias, and/or have used P-value-based stepwise variable selection (PSVS) to infer impacts, a strategy known to be poorly suited to the accurate estimation of regression coefficients. Broad-scale spatial autocorrelation has also generally been unaccounted for. We re-examine two UK observational datasets that have previously been used to investigate the relationship between Ndep and plant species richness in acid grasslands, a much-researched habitat in this context. One of these studies (Stevens et al., 2004, Science, 303: 1876–1879) estimated a large negative impact of Ndep on richness through the use of PSVS; the other reported smaller impacts (Maskell et al., 2010, Global Change Biology, 16: 671–679), but did not explicitly report regression coefficients or partial effects, making the actual size of the estimated Ndep impact difficult to assess. We reanalyse both datasets using a spatial Bayesian linear model estimated using integrated nested Laplace approximation (INLA). Contrary to previous results, we found similar-sized estimates of the Ndep impact on plant richness between studies, both with and without bryophytes, albeit with some disagreement over the most likely direction of this effect. Our analyses suggest that some previous estimates of Ndep impacts on richness from space-for-time substitution studies are likely to have been over-estimated, and that the evidence from observational studies could be fragile when confronted with alternative model specifications, although further work is required to investigate potentially nonlinear responses. Given the growing literature on the use of observational data to estimate the impacts of pollutants on biodiversity, we suggest that a greater focus on clearly reporting important outcomes with associated uncertainty, the use of techniques to account for spatial autocorrelation, and a clearer focus on the aims of a study, whether explanatory or predictive, are all required.

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<![CDATA[Purification, characterization and antioxidant activities in vitro of polysaccharides from <i>Amaranthus hybridus</i> L.]]> https://www.researchpad.co/article/elastic_article_12821 Amaranthus hybridus L. is an annual, erect or less commonly ascending herb that is a member of the Amaranthaceae family. Polysaccharides extracted from traditional Chinese medicines may be effective substances with antioxidant activity.MethodsIn this study, we isolated crude polysaccharides from A. hybridus (AHP-M) using microwave-assisted extraction. Then, the AHP-M was purified by chromatography with DEAE-32 cellulose, and two fractions, AHP-M-1 and AHP-M-2, were obtained. The structural characteristics of AHP-M-1 and AHP-M-2 were investigated, and their antioxidant activities were analyzed in vitro.ResultsWe found that the monosaccharide composition of AHP-M-1 was different from that of AHP-M-2. The molecular weights of AHP-M-1 and AHP-M-2 were 77.625 kDa and 93.325 kDa, respectively. The results showed that the antioxidant activity of AHP-M-2 was better than that of AHP-M-1. For AHP-M-2, the DPPH radical scavenging rate at a concentration of 2 mg/mL was 78.87%, the hydroxyl radical scavenging rate was 39.34%, the superoxide anion radical scavenging rate was 80.2%, and the reduction ability of Fe3+ was approximately 0.90. The total antioxidant capacity per milligram of AHP-M-2 was 6.42, which was higher than that of Vitamin C (Vc).ConclusionThe in vitro test indicated that AHP-M-1 and AHP-M-2 have good antioxidant activity, demonstrating that A. hybridus L. polysaccharide has immense potential as a natural antioxidants. ]]> <![CDATA[Soil water consumption, water use efficiency and winter wheat production in response to nitrogen fertilizer and tillage]]> https://www.researchpad.co/article/elastic_article_12769 Sustainability of winter wheat yield under dryland conditions depends on improving soil water stored during fallow and its efficient use. A 3-year field experiment was conducted in Loess Plateau to access the effect of tillage and N (nitrogen) rates on soil water, N distribution and water- and nitrogen-use efficiency of winter wheat. Deep tillage (DT, 25–30 cm depth) and no-tillage (NT) were operated during fallow season, whereas four N rates (0, 90, 150 and 210 kg ha−1) were applied before sowing. Rates of N and variable rainfall during summer fallow period led to the difference of soil water storage. Soil water storage at anthesis and maturity was decreased with increasing N rate especially in the year with high precipitation (2014–2015). DT has increased the soil water storage at sowing, N content, numbers of spike, grain number, 1,000 grain weight, grain yield, and water and N use efficiency as compared to NT. Grain yield was significantly and positively related to soil water consumption at sowing to anthesis and anthesis to maturity, total plant N, and water-use efficiency. Our study implies that optimum N rate and deep tillage during the fallow season could improve dryland wheat production by balancing the water consumption and biomass production.

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<![CDATA[Stomatal conductance bears no correlation with transpiration rate in wheat during their diurnal variation under high air humidity]]> https://www.researchpad.co/article/elastic_article_11279 A good understanding of the response of photosynthesis rate (PN) and transpiration rate (Tr) to stomatal alteration during the diurnal variations is important to cumulative photosynthetic production and water loss of crops. Six wheat genotypes were studied for 2 years with pot cultivation in rain-shelter. Among different genotypes, stomatal conductance (gs) was significantly correlated with both PN and Tr. But for each genotype, though gs was significantly correlated with PN regardless of relative air humidity (RH) status and it was also significantly correlated with Tr under lower RH (LRH, 15.4%) and moderate RH (MRH, 28.3%), it was not correlated with Tr under higher RH (HRH, 36.7%) during the diurnal changes. The conditional correlation between gs and Tr of wheat evoked new thinking on the relationships among gs, PN and Tr. Path analysis was further carried out to clarify the correlations of gs with the four atmospheric factors, that of Tr with gs and the four factors and the direct and indirect effects of the factors, during their diurnal dynamic variation. The effects of these factors on gs or Tr were related to RH. All the four factors had a much higher correlation with gs under HRH than that under LRH and MRH. Air temperature (T) had a rather higher direct effect than RH and photosynthetically active radiation (PAR). Also, the other factors had a much higher indirect effect on gs through vapor pressure deficit (VPD) and T. Transpiration rate was highly correlated with gs under LRH and MRH, with gs having a higher direct effect on it. In comparison, Tr was not correlated with gs under HRH but highly correlated with the atmospheric factors, with T, RH, and PAR having a higher indirect effect through VPD.

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<![CDATA[Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae]]> https://www.researchpad.co/article/elastic_article_11231 In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.

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<![CDATA[Extending thermotolerance to tomato seedlings by inoculation with SA1 isolate of <i>Bacillus cereus</i> and comparison with exogenous humic acid application]]> https://www.researchpad.co/article/elastic_article_11229 Heat stress is one of the major abiotic stresses that impair plant growth and crop productivity. Plant growth-promoting endophytic bacteria (PGPEB) and humic acid (HA) are used as bio-stimulants and ecofriendly approaches to improve agriculture crop production and counteract the negative effects of heat stress. Current study aimed to analyze the effect of thermotolerant SA1 an isolate of Bacillus cereus and HA on tomato seedlings. The results showed that combine application of SA1+HA significantly improved the biomass and chlorophyll fluorescence of tomato plants under normal and heat stress conditions. Heat stress increased abscisic acid (ABA) and reduced salicylic acid (SA) content; however, combined application of SA1+HA markedly reduced ABA and increased SA. Antioxidant enzymes activities revealed that SA1 and HA treated plants exhibited increased levels of ascorbate peroxidase (APX), superoxide dismutase (SOD), and reduced glutathione (GSH). In addition, heat stress markedly reduced the amino acid contents; however, the amino acids were increased with co-application of SA1+HA. Similarly, inductively-coupled plasma mass-spectrometry results showed that plants treated with SA1+HA exhibited significantly higher iron (Fe+), phosphorus (P), and potassium (K+) uptake during heat stress. Heat stress increased the relative expression of SlWRKY33b and autophagy-related (SlATG5) genes, whereas co-application of SA1+HA augmented the heat stress response and reduced SlWRKY33b and SlATG5 expression. The heat stress-responsive transcription factor (SlHsfA1a) and high-affinity potassium transporter (SlHKT1) were upregulated in SA1+HA-treated plants. In conclusion, current findings suggest that co-application with SA1+HA can be used for the mitigation of heat stress damage in tomato plants and can be commercialized as a biofertilizer.

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<![CDATA[Flavonoids and antioxidant activity of rare and endangered fern: <i>Isoetes sinensis</i>]]> https://www.researchpad.co/article/elastic_article_7844 Isoetes sinensis Palmer is a critically endangered, first-class protected plant in China. Until now, researchers have primarily focused on the ultrastructure, phylogeny, and transcriptomes of the plant. However, flavonoid profiles and bioactivity of I. sinensis have not been extensively investigated. To develop the endangered I. sinensis for edible and medicinal purposes, flavonoid content, chemical constitution, and antioxidant activities were investigated in this study. Results revealed the following. 1) The total flavonoid content was determined as 10.74 ± 0.25 mg/g., 2) Antioxidant activities were stronger than most ferns, especially ABTS free radical scavenging activities. 3) Four flavones, containing apigenin, apigenin-7-glucuronide, acacetin-7-O-glcopyranoside, and homoplantageninisoetin; four flavonols, namely, isoetin, kaempferol-3-O-glucoside, quercetin-3-O-[6”-O-(3-hydroxy-3-methylglutaryl)-β-D-glucopyranoside], and limocitrin-Neo; one prodelphinidin (procyanidins;) and one nothofagin (dihydrochalcone) were tentatively identified in the mass spectrometry-DAD (254nm) chromatograms. This study was the first to report on flavonoid content and antioxidant activities of I. sinensis. Stronger antioxidant activity and flavonoid content suggests that the endangered I. sinensis is an important and potentially edible and medicinal plant.

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<![CDATA[Imaging dataset of fresh hydrous plants obtained by field-emission scanning electron microscopy conducted using a protective NanoSuit]]> https://www.researchpad.co/article/elastic_article_7644 Although scanning electron microscopy (SEM) can generate high-resolution images of nanosized objects, it requires a high vacuum to do so, which precludes direct observations of living organisms and often produces unwanted structural changes. It has previously been reported that a simple surface modification gives rise to a nanoscale layer, termed the “NanoSuit”, which can keep small animals alive under the high vacuum required for field-emission scanning electron microscopy (FE-SEM). We have previously applied this technique to plants, and successfully observed healthy petals in a fully hydrated state using SEM. The flower petals protected with the NanoSuit appeared intact, although we still lack a fundamental understanding of the images of other plants observed using FE-SEM. This report presents and evaluates a rich set of images, acquired using the NanoSuit, for a taxonomically diverse set of plant species. This dataset of images allows the surface features of various plants to be analyzed and thus provides a further complementary morphological profile. Image data can be accessed and viewed through Figshare (https://doi.org/10.6084/m9.figshare.c.4446026.v1).

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<![CDATA[Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush)]]> https://www.researchpad.co/article/elastic_article_8415 This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations.LocationThe Cape Floristic Region (CFR), located along the southern Cape of South Africa.MethodsPolymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored.ResultsWe present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases with distance (p < 0.05 for IBD analyses).ConclusionsAfter screening for regions with high HRM clustering specificity—akin to the screening process associated with most PCR based markers—the technology was found to be a high throughput tool for detecting genetic variation in non-model plants. ]]> <![CDATA[Depigmenting potential of lichen extracts evaluated by in vitro and in vivo tests]]> https://www.researchpad.co/article/elastic_article_8410 Melanin is the main pigment of human skin, playing the primary role of protection from ultraviolet radiation. Alteration of the melanin production may lead to hyperpigmentation diseases, with both aesthetic and health consequences. Thus, suppressors of melanogenesis are considered useful tools for medical and cosmetic treatments. A great interest is focused on natural sources, aimed at finding safe and quantitatively available depigmenting substances. Lichens are thought to be possible sources of this kind of compounds, as the occurrence of many phenolic molecules suggests possible effects on phenolase enzymes involved in melanin synthesis, like tyrosinase. In this work, we used four lichen species, Cetraria islandica Ach., Flavoparmelia caperata Hale, Letharia vulpina (L.) Hue, and Parmotrema perlatum (Hudson) M. Choisy, to obtain extracts in solvents of increasing polarity, viz. chloroform, chloroform-methanol, methanol, and water. Cell-free, tyrosinase inhibition experiments showed highest inhibition for L. vulpina methanol extract, followed by C. islandica chloroform-methanol one. Comparable results for depigmenting activities were observed by means of in vitro and in vivo systems, such as MeWo melanoma cells and zebrafish larvae. Our study provides first evidence of depigmenting effects of lichen extracts, from tyrosinase inhibition to cell and in vivo models, suggesting that L. vulpina and C. islandica extracts deserve to be further studied for developing skin-whitening products.

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<![CDATA[Full-length transcriptome and targeted metabolome analyses provide insights into defense mechanisms of <i>Malus sieversii</i> against <i>Agrilus mali</i>]]> https://www.researchpad.co/article/elastic_article_8337 Malus sieversii is the wild progenitor for many cultivars of domesticated apple and an important germplasm resource for breeding. However, this valuable species faces a significant threat in the areas north of the Tianshan Mountains in China, by the invasion of Agrilus mali, a destructive pest of apple trees belonging to the family Buprestidae. Our preliminary study has has shown that there may be resistance to this insect in M. sieversii plants in the field, but the corresponding molecular mechanisms remain unclear. In this study, we compared the response of insect-resistant and insect-susceptible plants of M. sieversii to insect feeding using full-length transcriptome and targeted metabolome. 112,103 non-chimeric full-length reads (FLNC) totaling 10.52 Gb of data were generating with Pacific Biosciences SingleMolecule, Real-Time (PacBio SMRT) sequencing. A total of 130.06 Gb data of long reads were acquired with an Illumina HiSeq. Function annotation indicated that the different expressed genes (DEGs) were mainly involved in signal transduction pathway of plant hormones and in the synthesis of compounds such as terpenes, quinones, flavonoids, and jasmonic acid. Through targeted metabolome analysis resistant strains showed higher levels of trans-cinnamic acid, caffeine and ferulic acid after pest infestation. This study helps to decipher the transcriptional changes and related signaling paths in M. sieversii after an insect feeding, which lays a foundation for further research on molecular mechanisms of insect resistance in apples.

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<![CDATA[Genome-wide identification and characterization of TCP family genes in <i>Brassica juncea</i> var. tumida]]> https://www.researchpad.co/article/elastic_article_8329 Teosinte branched1/Cycloidea/proliferating cell factors (TCPs) are plant-specific transcription factors widely involved in leaf development, flowering, shoot branching, the circadian rhythm, hormone signaling, and stress responses. However, the TCP function in Brassica juncea var. tumida, the tumorous stem mustard, has not yet been reported. This study identified and characterized the entire TCP family members in B. juncea var. tumida.MethodsWe identified 62 BjTCP genes from the B. juncea var. tumida genome and analyzed their phylogenetic relationship, gene structure, protein motifs, chromosome location, and expression profile in different tissues.ResultsOf the 62 BjTCP genes we identified in B. juncea var. tumida, containing 34 class I and 28 class II subfamily members, 61 were distributed on 18 chromosomes. Gene structure and conserved motif analysis showed that the same clade genes displayed a similar exon/intron gene structure and conserved motifs. Cis-acting element results showed that the same clade genes also had a similar cis-acting element; however, subtle differences implied a different regulatory pathway. The BjTCP18s members were low-expressed in Dayejie strains and the unswelling stage of Yonganxiaoye strains. Treatment with gibberellin (GA) and salicylic acid (SA) showed that GA and SA affect the expression levels of multiple TCP genes.ConclusionWe performed the first genome-wide analysis of the TCP gene family of B. juncea var. tumida. Our results have provided valuable information for understanding the classification and functions of TCP genes in B. juncea var. tumida. ]]>