Anhui Agricultural University

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

Highly efficient removal of metal ion pollutants, such as toxic and nuclear waste-related metal ions, remains a serious task from the biological and environmental standpoint because of their harmful effects on human health and the environment. Recently, highly porous metal-organic frameworks (MOFs), with excellent chemical stability and abundant functional groups, have represented a new addition to the area of capturing various types of hazardous metal ion pollutants. This review focuses on recent progress in reported MOFs and MOF-based composites as superior adsorbents for the efficient removal of toxic and nuclear waste-related metal ions. Aspects related to the interaction mechanisms between metal ions and MOF-based materials are systematically summarized, including macroscopic batch experiments, microscopic spectroscopy analysis, and theoretical calculations. The adsorption properties of various MOF-based materials are assessed and compared with those of other widely used adsorbents. Finally, we propose our personal insights into future research opportunities and challenges in the hope of stimulating more researchers to engage in this new field of MOF-based materials for environmental pollution management.

(CSA), is calculated to ∼0.38 to 1.54 million years ago (Mya). Analysis of genic collinearity reveals that the tea genome is the product of two rounds of whole-genome duplications (WGDs) that occurred ∼30 to 40 and ∼90 to 100 Mya. We provide evidence that these WGD events, and subsequent paralogous duplications, had major impacts on the copy numbers of secondary metabolite genes, particularly genes critical to producing three key quality compounds: catechins, theanine, and caffeine. Analyses of transcriptome and phytochemistry data show that amplification and transcriptional divergence of genes encoding a large acyltransferase family and leucoanthocyanidin reductases are associated with the characteristic young leaf accumulation of monomeric galloylated catechins in tea, while functional divergence of a single member of the glutamine synthetase gene family yielded theanine synthetase. This genome sequence will facilitate understanding of tea genome evolution and tea metabolite pathways, and will promote germplasm utilization for breeding improved tea varieties.

The bactericidal action of silver (0) nanoparticles and amoxicillin on Escherichia coli is studied, respectively. Increasing concentration of both amoxicillin (0–0.525 mg ml−1) and silver nanoparticles (0–40 µg ml−1) showed a higher antibacterial effect in Luria–Bertani (LB) medium. Escherichia coli cells have different bactericidal sensitivity to them. When amoxicillin and silver nanoparticles are combined, it results in greater bactericidal efficiency on Escherichia coli cells than when they were applied separately. Dynamic tests on bacterial growth indicated that exponential and stationary phases are greatly decreased and delayed in the synergistic effect of amoxicillin and silver nanoparticles. In addition, the effect induced by a preincubation with silver nanoparticles is examined. The results show that solutions with more silver nanoparticles have better antimicrobial effects. One hypothesized mechanism is proposed to explain this phenomenon.

Tea is a typical processed beverage from the fresh leaves of Camellia sinensis [Camellia sinensis (L.) O. Kuntze] or Camellia assamica [Camellia sinensis var. assamica (Mast.) Kitamura] through different manufacturing techniques. The secondary metabolites of fresh tea leaves are mainly flavan-3-ols, phenolic acids, purine alkaloids, condensed tannins, hydrolysable tannins, saponins, flavonols, and their glycoside forms. During the processing, tea leaves go through several steps, such as withering, rolling, fermentation, postfermentation, and roasting (drying) to produce different types of tea. After processing, theaflavins, thearubigins, and flavan-3-ols derivatives emerge as the newly formed compounds with a corresponding decrease in concentrations of catechins. Each type of tea has its own critical process and presents unique chemical composition and flavor. The components among different teas also cause significant changes in their biological activities both in vitro and in vivo. In the present review, the progress of tea chemistry and the effects of individual unit operation on components were comprehensively described. The health benefits of tea were also reviewed based on the human epidemiological and clinical studies. Although there have been multiple studies about the tea chemistry and biological activities, most of existing results are related to tea polyphenols, especially (-)-epigallocatechin gallate. Other compounds, including the novel compounds, as well as isomers of amino acids and catechins, have not been explored in depth.

Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.

The ever increasing production and use of nano-enabled commercial products release the massive amount of engineered nanoparticles (ENPs) in the environment. An increasing number of recent studies have shown the toxic effects of ENPs on different organisms, raising concerns over the nano-pollutants behavior and fate in the various environmental compartments. After the release of ENPs in the environment, ENPs interact with various components of the environment and undergoes dynamic transformation processes. This review focus on ENPs transformations in the various environmental compartments. The transformation processes of ENPs are interrelated to multiple environmental aspects. Physical, chemical and biological processes such as the homo- or hetero-agglomeration, dissolution/sedimentation, adsorption, oxidation, reduction, sulfidation, photochemically and biologically mediated reactions mainly occur in the environment consequently changes the mobility and bioavailability of ENPs. Physico-chemical characteristics of ENPs (particle size, surface area, zeta potential/surface charge, colloidal stability, and core-shell composition) and environmental conditions (pH, ionic strength, organic and inorganic colloids, temperature, etc.) are the most important parameters which regulated the ENPs environmental transformations. Meanwhile, in the environment, organisms encountered multiple transformed ENPs rather than the pristine nanomaterials due to their interactions with various environmental materials and other pollutants. Thus it is the utmost importance to study the behavior of transformed ENPs to understand their environmental fate, bioavailability, and mode of toxicity.

BACKGROUND: Tea is one of the most popular non-alcoholic beverages worldwide. However, the tea plant, Camellia sinensis, is difficult to culture in vitro, to transform, and has a large genome, rendering little genomic information available. Recent advances in large-scale RNA sequencing (RNA-seq) provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes. RESULTS: Using high-throughput Illumina RNA-seq, the transcriptome from poly (A)+ RNA of C. sinensis was analyzed at an unprecedented depth (2.59 gigabase pairs). Approximate 34.5 million reads were obtained, trimmed, and assembled into 127,094 unigenes, with an average length of 355 bp and an N50 of 506 bp, which consisted of 788 contig clusters and 126,306 singletons. This number of unigenes was 10-fold higher than existing C. sinensis sequences deposited in GenBank (as of August 2010). Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 55,088 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. Some of the unigenes were assigned to putative metabolic pathways. Targeted searches using these annotations identified the majority of genes associated with several primary metabolic pathways and natural product pathways that are important to tea quality, such as flavonoid, theanine and caffeine biosynthesis pathways. Novel candidate genes of these secondary pathways were discovered. Comparisons with four previously prepared cDNA libraries revealed that this transcriptome dataset has both a high degree of consistency with previous EST data and an approximate 20 times increase in coverage. Thirteen unigenes related to theanine and flavonoid synthesis were validated. Their expression patterns in different organs of the tea plant were analyzed by RT-PCR and quantitative real time PCR (qRT-PCR). CONCLUSIONS: An extensive transcriptome dataset has been obtained from the deep sequencing of tea plant. The coverage of the transcriptome is comprehensive enough to discover all known genes of several major metabolic pathways. This transcriptome dataset can serve as an important public information platform for gene expression, genomics, and functional genomic studies in C. sinensis.

Climate change, food shortage, water scarcity, and population growth are some of the threatening challenges being faced in today’s world. Drought stress (DS) poses a constant challenge for agricultural crops and has been considered a severe constraint for global agricultural productivity; its intensity and severity are predicted to increase in the near future. Legumes demonstrate high sensitivity to DS, especially at vegetative and reproductive stages. They are mostly grown in the dry areas and are moderately drought tolerant, but severe DS leads to remarkable production losses. The most prominent effects of DS are reduced germination, stunted growth, serious damage to the photosynthetic apparatus, decrease in net photosynthesis, and a reduction in nutrient uptake. To curb the catastrophic effect of DS in legumes, it is imperative to understand its effects, mechanisms, and the agronomic and genetic basis of drought for sustainable management. This review highlights the impact of DS on legumes, mechanisms, and proposes appropriate management approaches to alleviate the severity of water stress. In our discussion, we outline the influence of water stress on physiological aspects (such as germination, photosynthesis, water and nutrient uptake), growth parameters and yield. Additionally, mechanisms, various management strategies, for instance, agronomic practices (planting time and geometry, nutrient management), plant growth-promoting Rhizobacteria and arbuscular mycorrhizal fungal inoculation, quantitative trait loci (QTLs), functional genomics and advanced strategies (CRISPR-Cas9) are also critically discussed. We propose that the integration of several approaches such as agronomic and biotechnological strategies as well as advanced genome editing tools is needed to develop drought-tolerant legume cultivars.

Tea, a popular beverage made from leaves of the plant Camellia sinensis, has been shown to reduce body weight, alleviate metabolic syndrome, and prevent diabetes and cardiovascular diseases in animal models and humans. Such beneficial effects have generally been observed in most human studies when the level of tea consumption was three to four cups (600-900 mg tea catechins) or more per day. Green tea is more effective than black tea. In spite of numerous studies, the fundamental mechanisms for these actions still remain unclear. From a review of the literature, we propose that the two major mechanisms are: (i) decreasing absorption of lipids and proteins by tea constituents in the intestine, thus reducing calorie intake; and (ii) activating AMP-activated protein kinase by tea polyphenols that are bioavailable in the liver, skeletal muscle, and adipose tissues. The relative importance of these two mechanisms depends on the types of tea and diet consumed by individuals. The activated AMP-activated protein kinase would decrease gluconeogenesis and fatty acid synthesis and increase catabolism, leading to body weight reduction and metabolic syndrome alleviation. Other mechanisms and the health relevance of these beneficial effects of tea consumption remain to be further investigated.

Abstract Invasive alien plant species threaten native biodiversity, disrupt ecosystem functions and can cause large economic damage. Plant invasions have been predicted to further increase under ongoing global environmental change. Numerous case studies have compared the performance of invasive and native plant species in response to global environmental change components (i.e. changes in mean levels of precipitation, temperature, atmospheric CO 2 concentration or nitrogen deposition). Individually, these studies usually involve low numbers of species and therefore the results cannot be generalized. Therefore, we performed a phylogenetically controlled meta‐analysis to assess whether there is a general pattern of differences in invasive and native plant performance under each component of global environmental change. We compiled a database of studies that reported performance measures for 74 invasive alien plant species and 117 native plant species in response to one of the above‐mentioned global environmental change components. We found that elevated temperature and CO 2 enrichment increased the performance of invasive alien plants more strongly than was the case for native plants. Invasive alien plants tended to also have a slightly stronger positive response to increased N deposition and increased precipitation than native plants, but these differences were not significant (N deposition: P = 0.051; increased precipitation: P = 0.679). Invasive alien plants tended to have a slightly stronger negative response to decreased precipitation than native plants, although this difference was also not significant ( P = 0.060). So while drought could potentially reduce plant invasion, increases in the four other components of global environmental change considered, particularly global warming and atmospheric CO 2 enrichment, may further increase the spread of invasive plants in the future.

Tea is among the most consumed nonalcoholic beverages worldwide. Understanding tea flavor, in terms of both sensory aspects and chemical properties, is essential for manufacturers and consumers to maintain high quality of tea products and to correctly distinguish acceptable or unacceptable products. This article gives a comprehensive review on the aroma and off-flavor characteristics associated with 184 odorants. Although many efforts have been made toward the characterization of flavor compounds in different types of tea, modern flavor analytical techniques that affect the results of flavor analysis have not been compared and summarized systematically up to now. Thus, the overview mainly provides the instrumental flavor analytical techniques for both aroma and taste of tea (i.e., extraction and enrichment, qualitative, quantitative, and chemometric approaches) as well as descriptive sensory analytical methodologies for tea, which is helpful for tea flavor researchers. Flavor developments of tea evolved toward time-saving, portability, real-time monitoring, and visualization are also prospected to get a deeper insight into the influences of different processing techniques on the formation and changes of flavor compounds, especially desired flavor compounds and off-flavor substances present at (ultra)trace amounts in tea and tea products.

The ending of dual nomenclatural systems for pleomorphic fungi in 2011 requires the reconciliation of competing names, ideally linked through culture based or molecular methods. The phylogenetic systematics of Hypocreales and its many genera have received extensive study in the last two decades, however resolution of competing names in Cordycipitaceae has not yet been addressed. Here we present a molecular phylogenetic investigation of Cordycipitaceae that enables identification of competing names in this family, and provides the basis upon which these names can be maintained or suppressed. The taxonomy presented here seeks to harmonize competing names by principles of priority, recognition of monophyletic groups, and the practical usage of affected taxa. In total, we propose maintaining nine generic names, Akanthomyces, Ascopolyporus, Beauveria, Cordyceps, Engyodontium, Gibellula, Hyperdermium, Parengyodontium, and Simplicillium and the rejection of eight generic names, Evlachovaea, Granulomanus, Isaria, Lecanicillium, Microhilum, Phytocordyceps, Synsterigmatocystis, and Torrubiella. Two new generic names, Hevansia and Blackwellomyces, and a new species, Beauveria blattidicola, are described. New combinations are also proposed in the genera Akanthomyces, Beauveria, Blackwellomyces, and Hevansia.

Plastic pollution is a global concern given its prevalence in aquatic and terrestrial ecosystems. Studies have been conducted on the distribution and impact of plastic pollution in marine ecosystems, but little is known on terrestrial ecosystems. Plastic mulch has been widely used to increase crop yields worldwide, yet the impact of plastic residues in cropland soils to soil health and crop production in the long term remained unclear. In this paper, using a global meta-analysis, we found that the use of plastic mulch can indeed increase crop yields on average by 25%-42% in the immediate season due to the increase of soil temperature (+8%) and moisture (+17%). However, the unabated accumulation of film residues in the field negatively impacts its physicochemical properties linked to healthy soil and threatens food production in the long term. It has multiple negative impacts on plant growth including crop yield (at the mean rate of -3% for every additional 100 kg/ha of film residue), plant height (-2%) and root weight (-5%), and soil properties including soil water evaporation capacity (-2%), soil water infiltration rate (-8%), soil organic matter (-0.8%) and soil available phosphorus (-5%) based on meta-regression. Using a nationwide field survey of China, the largest user of plastic mulch worldwide, we found that plastic residue accumulation in cropland soils has reached 550,800 tonnes, with an estimated 6%-10% reduction in cotton yield in some polluted sites based on current level of plastic residue content. Immediate actions should be taken to ensure the recovery of plastic film mulch and limit further increase in film residue loading to maintain the sustainability of these croplands.

Salinity is a global challenge to agricultural production. Understanding Na+ sensing and transport in plants under salt stress will be of benefit for breeding robustly salt-tolerant crop species. In this review, first, possible salt stress sensor candidates and the root meristem zone as a tissue harboring salt stress-sensing components are proposed. Then, the importance of Na+ exclusion and vacuolar Na+ sequestration in plant overall salt tolerance is highlighted. Other Na+ regulation processes, including xylem Na+ loading and unloading, phloem Na+ recirculation, and Na+ secretion, are discussed and summarized. Along with a summary of Na+ transporters and channels, the molecular regulation of Na+ transporters and channels in response to salt stress is discussed. Finally, some largely neglected issues in plant salt stress tolerance, including Na+ concentration in cytosol and the role of Na+ as a nutrient, are reviewed and discussed.

MYB transcription factors (TFs), as one of the largest gene families in plants, play important roles in multiple biological processes, such as plant growth and development, cell morphology and pattern building, physiological activity metabolism, primary and secondary metabolic reactions, and responses to environmental stresses. The function of MYB TFs in crops has been widely studied, but few studies have been done on medicinal plants. In this review, we summarized the MYB TFs that play important roles in secondary metabolism and emphasized the possible mechanisms underlying how MYB TFs are regulated at the protein, posttranscriptional, and transcriptional levels, as well as how they regulate the downstream target gene networks related to secondary metabolism in plants, especially in medicinal plants.

Tea is the world's widely consumed nonalcohol beverage with essential economic and health benefits. Confronted with the increasing large-scale omics-data set particularly the genome sequence released in tea plant, the construction of a comprehensive knowledgebase is urgently needed to facilitate the utilization of these data sets towards molecular breeding. We hereby present the first integrative and specially designed web-accessible database, Tea Plant Information Archive (TPIA; http://tpia.teaplant.org). The current release of TPIA employs the comprehensively annotated tea plant genome as framework and incorporates with abundant well-organized transcriptomes, gene expressions (across species, tissues and stresses), orthologs and characteristic metabolites determining tea quality. It also hosts massive transcription factors, polymorphic simple sequence repeats, single nucleotide polymorphisms, correlations, manually curated functional genes and globally collected germplasm information. A variety of versatile analytic tools (e.g. JBrowse, blast, enrichment analysis, etc.) are established helping users to perform further comparative, evolutionary and functional analysis. We show a case application of TPIA that provides novel and interesting insights into the phytochemical content variation of section Thea of genus Camellia under a well-resolved phylogenetic framework. The constructed knowledgebase of tea plant will serve as a central gateway for global tea community to better understand the tea plant biology that largely benefits the whole tea industry.

), respectively, owing to a synergetic quadruple dynamic mechanism. It is revealed that the B-N coordination not only facilitates the formation and dissociation of boronic ester at room temperature but also dramatically enhances the mechanical properties by the intermolecular coordinated chain crosslinking and intramolecular coordinated chain folding. Meanwhile, the B-N coordination and urethane hydrogen interaction also serve as sacrificial bonds, which rupture during stretching to dissipate energy and recover after release, leading to superior notch insensitiveness and recoverability. The SPUEs restore their mechanical robustness after self-healing at room temperature and the self-healing efficiency can be dramatically accelerated by surface wetting.

Rapid and early diagnosis of respiratory viruses is key to preventing infections from spreading and guiding treatments. Here, we developed a sensitive and quantitative surface-enhanced Raman scattering-based lateral flow immunoassay (SERS-based LFIA) strip for simultaneous detection of influenza A H1N1 virus and human adenovirus (HAdV) by using Fe3O4@Ag nanoparticles as magnetic SERS nanotags. The new type of Fe3O4@Ag magnetic tags, which were conjugated with dual-layer Raman dye molecules and target virus-capture antibodies, performs the following functions: specific recognition and magnetic enrichment of target viruses in the solution and SERS detection of the viruses on the strip. Based on this strategy, the magnetic SERS strip can directly be used for real biological samples without any sample pretreatment steps. The limits of detection for H1N1 and HAdV were 50 and 10 pfu/mL, respectively, which were 2000 times more sensitive than those from the standard colloidal gold strip method. Moreover, the proposed strip is easy to operate, rapid, stable, and can achieve high throughput and is thus a potential tool for early detection of virus infection.

Abstract A high-quality genome is the basis for studies on functional, evolutionary, and comparative genomics. The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences, along with the emergence of a new ‘telomere-to-telomere (T2T) assembly’ era. However, the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited. Here, we developed a user-friendly web toolkit, quarTeT, which currently includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. First, AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome. Then, GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences. Finally, TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome. These four modules can be used alone or in combination with each other for T2T genome assembly and characterization. As a case study, by adopting the entire modular functions of quarTeT, we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0, which was assembled with the addition of manual handling. Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods. Collectively, quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.