Complete genome sequence of Paracidovorax avenae causing red stripe in sugarcane.

OBJECTIVE: Paracidovorax avenae (Pa) is the causative agent of red stripe disease in sugarcane and belongs to the Gram-negative ß-Proteobacteria. Red stripe is a major bacterial disease of sugarcane worldwide. Limited genome sequences of Pa can be used for exploring the phylogenetic and genetic diversity analysis in this pathogen at the complete genome level. In this study, a whole genome sequence of Pa CNGX08 strain isolated from sugarcane in China was assembled and annotated. DATA DESCRIPTION: Genome assembly data from second- and third-generation sequencing revealed that the entire genomic sequence of Pa CNGX08 strain causing red stripe in sugarcane, consisted of a 5,625,582 bp circular chromosome with a GC content of 68.97%. In total, 4,915 protein-coding genes were annotated. Additionally, 9 ribosomal RNAs and 52 transfer RNAs were identified. This genomic resource will facilitate the genome-based taxonomic classification of the genus Paracidovorax and the exploration of pathogenic mechanisms underlying sugarcane red stripe disease caused by Pa.

Insights into Reactive Oxygen Species Production-Scavenging System Involved in Sugarcane Response to Xanthomonas albilineans Infection under Drought Stress.

Plants must adapt to the complex effects of several stressors brought on by global warming, which may result in interaction and superposition effects between diverse stressors. Few reports are available on how drought stress affects Xanthomonas albilineans (Xa) infection in sugarcane (Saccharum spp. hybrids). Drought and leaf scald resistance were identified on 16 sugarcane cultivars using Xa inoculation and soil drought treatments, respectively. Subsequently, four cultivars contrasting to drought and leaf scald resistance were used to explore the mechanisms of drought affecting Xa-sugarcane interaction. Drought stress significantly increased the occurrence of leaf scald and Xa populations in susceptible cultivars but had no obvious effect on resistant cultivars. The ROS bursting and scavenging system was significantly activated in sugarcane in the process of Xa infection, particularly in the resistant cultivars. Compared with Xa infection alone, defense response via the ROS generating and scavenging system was obviously weakened in sugarcane (especially in susceptible cultivars) under Xa infection plus drought stress. Collectively, ROS might play a crucial role involving sugarcane defense against combined effects of Xa infection and drought stress.

Genetic Divergence and Population Structure of Xanthomonas albilineans Strains Infecting Saccharum spp. Hybrid and Saccharum officinarum.

Leaf scald caused by Xanthomonas albilineans (Xa) is a major bacterial disease in sugarcane that represents a threat to the global sugar industry. Little is known about the population structure and genetic evolution of this pathogen. In this study, 39 Xa strains were collected from 6 provinces in China. Of these strains, 15 and 24 were isolated from Saccharum spp. hybrid and S. officinarum plants, respectively. Based on multilocus sequence analysis (MLSA), with five housekeeping genes, these strains were clustered into two distinct phylogenetic groups (I and II). Group I included 26 strains from 2 host plants, Saccharum spp. hybrid and S. officinarum collected from 6 provinces, while Group II consisted of 13 strains from S. officinarum plants in the Zhejiang province. Among the 39 Xa strains, nucleotide sequence identities from 5 housekeeping genes were: ABC (99.6-100%), gyrB (99.3-100%), rpoD (98.4-100%), atpD (97.0-100%), and glnA (97.6-100%). These strains were clustered into six groups (A-F), based on the rep-PCR fingerprinting, using primers for ERIC2, BOX A1R, and (GTG)5. UPGMA and PCoA analyses revealed that group A had the most strains (24), followed by group C with 11 strains, while there was 1 strain each in groups B and D-F. Neutral tests showed that the Xa population in S. officinarum had a trend toward population expansion. Selection pressure analysis showed purification selection on five concatenated housekeeping genes from all tested strains. Significant genetic differentiation and infrequent gene flow were found between two Xa populations hosted in Saccharum spp. hybrids and S. officinarum. Altogether, these results provide evidence of obvious genetic divergence and population structures among Xa strains from China.

Genetic and morphological variants of Acidovorax avenae subsp. avenae cause red stripe of sugarcane in China.

Sugarcane (Saccharum spp.) is an important cash crop for production of sugar and bioethanol. Red stripe caused by Acidovorax avenae subsp. avenae (Aaa) is a disease that occurs in numerous sugarcane-growing regions worldwide. In this study, 17 strains of Aaa were isolated from 13 symptomatic leaf samples in China. Nine of these strains produced white-cream colonies on nutrient agar medium while the other eight produced yellow colonies. In pairwise sequence comparisons of the 16S-23S rRNA internally transcribed spacer (ITS), the 17 strains had 98.4-100% nucleotide identity among each other and 98.2-99.5% identity with the reference strain of Aaa (ATCC 19860). Three RFLP patterns based on this ITS sequence were also found among the strains of Aaa obtained in this study. Multilocus sequence typing (MLST) based on five housekeeping genes (ugpB, pilT, lepA, trpB, and gltA) revealed that the strains of Aaa from sugarcane in China and a strain of Aaa (30179) isolated from sorghum in Brazil formed a unique evolutionary subclade. Twenty-four additional strains of Aaa from sugarcane in Argentina and from other crops worldwide were distributed in two other and separate subclades, suggesting that strains of A. avenae from sugarcane are clonal populations with local specificities. Two strains of Aaa from China (CNGX08 forming white-cream colored colonies and CNGD05 forming yellow colonies) induced severe symptoms of red stripe in sugarcane varieties LC07-150 and ZZ8 but differed based on disease incidence in two separate inoculation experiments. Infected plants also exhibited increased salicylic acid (SA) content and transcript expression of gene PR-1, indicating that the SA-mediated signal pathway is involved in the response to infection by Aaa. Consequently, red stripe of sugarcane in China is caused by genetically different strains of Aaa and at least two morphological variants. The impact of these independent variations on epidemics of red stripe remains to be investigated.

Systematic and functional analysis of non-specific lipid transfer protein family genes in sugarcane under Xanthomonas albilineans infection and salicylic acid treatment.

Plant non-specific lipid transfer proteins (nsLTPs) are small basic proteins that play a significant regulatory role in a wide range of physiological processes. To date, no genome-wide survey and expression analysis of this gene family in sugarcane has been performed. In this study we identified the nsLTP gene family in Saccharum spontaneum and carried out expression profiling of nsLTPs in two sugarcane cultivars (Saccharum spp.) that have different resistance to leaf scald caused by Xanthomonas albilineans (Xa) infection. The effect of stress related to exogenous salicylic acid (SA) treatment was also examined. At a genome-wide level, S. spontaneum AP85-441 had 71 SsnsLTP genes including 66 alleles. Tandem (9 gene pairs) and segmental (36 gene pairs) duplication events contributed to SsnsLTP gene family expansion. Five SsnsLTP proteins were predicted to interact with five other proteins. Expression of ShnsLTPI.8/10/Gb.1 genes was significantly upregulated in LCP85-384 (resistant cultivar), but downregulated in ROC20 (susceptible cultivar), suggesting that these genes play a positive regulatory role in response of sugarcane to Xa infection. Conversely, ShnsLTPGa.4/Ge.3 appears to act as a negative regulator in response Xa infection. The majority (16/17) of tested genes were positively induced in LCP85-384 72 h after SA treatment. In both cultivars, but particularly in LCP85-384, ShnsLTPIV.3/VIII.1 genes were upregulated at all time-points, suggesting that the two genes might act as positive regulators under SA stress. Meanwhile, both cultivars showed downregulated ShnsLTPGb.1 gene expression, indicating its potential negative role in SA treatment responses. Notably, the ShnsLTPGb.1 gene had contrasting effects, with positive regulation of gene expression in response to Xa infection and negative regulation induced by SA stress. Together, our results provide valuable information for elucidating the function of ShnsLTP family members under two stressors and identified novel gene sources for development of sugarcane that are tolerant of environmental stimuli.

Sugarcane responses to two strains of Xanthomonas albilineans differing in pathogenicity through a differential modulation of salicylic acid and reactive oxygen species.

Leaf scald caused by Xanthomonas albilineans is one of the major bacterial diseases of sugarcane that threaten the sugar industry worldwide. Pathogenic divergence among strains of X. albilineans and interactions with the sugarcane host remain largely unexplored. In this study, 40 strains of X. albilineans from China were distributed into three distinct evolutionary groups based on multilocus sequence analysis and simple sequence repeats loci markers. In pathogenicity assays, the 40 strains of X. albilineans from China were divided into three pathogenicity groups (low, medium, and high). Twenty-four hours post inoculation (hpi) of leaf scald susceptible variety GT58, leaf populations of X. albilineans strain XaCN51 (high pathogenicity group) determined by qPCR were 3-fold higher than those of strain XaCN24 (low pathogenicity group). Inoculated sugarcane plants modulated the reactive oxygen species (ROS) homoeostasis by enhancing respiratory burst oxidase homolog (ScRBOH) expression and superoxide dismutase (SOD) activity and by decreasing catalase (CAT) activity, especially after infection by X. albilineans XaCN51. Furthermore, at 24 hpi, plants infected with XaCN51 maintained a lower content of endogenous salicylic acid (SA) and a lower expression level of SA-mediated genes (ScNPR3, ScTGA4, ScPR1, and ScPR5) as compared to plants infected with XaCN24. Altogether, these data revealed that the ROS production-scavenging system and activation of the SA pathway were involved in the sugarcane defense response to an attack by X. albilineans.

Molecular Detection and Quantification of Xanthomonas albilineans in Juice from Symptomless Sugarcane Stalks Using a Real-Time Quantitative PCR Assay.

Leaf scald, a bacterial disease caused by Xanthomonas albilineans (Ashby) Dowson, is a major limiting factor for sugarcane production worldwide. Accurate identification and quantification of X. albilineans is a prerequisite for successful management of this disease. A sensitive and robust quantitative PCR (qPCR) assay was developed in this study for detection and quantification of X. albilineans using TaqMan probe and primers targeting a putative adenosine triphosphate-binding cassette (ABC) transporter gene (abc). The novel qPCR assay was highly specific to the 43 tested X. albilineans strains belonging to different pulsed-field gel electrophoresis groups. The detection thresholds were 100 copies/µl of plasmid DNA, 100 fg/µl of bacterial genomic DNA, and 100 CFU/ml of bacterial suspension prepared from pure culture. This qPCR assay was 100 times more sensitive than a conventional PCR assay. The pathogen was detected by qPCR in 75.1% (410/546) of symptomless stalk samples, whereas only 28.4% (155/546) of samples tested positive by conventional PCR. Based on qPCR data, population densities of X. albilineans in symptomless stalks of the same varieties differed between two sugarcane production areas in China, Beihai (Guangxi Province) and Zhanjiang (Guangdong Province), and no significant correlation between these populations was identified. Furthermore, no relationship was found between these populations of the pathogen in asymptomatic stalks and the resistance level of the sugarcane varieties to leaf scald. The newly developed qPCR assay proved to be highly sensitive and reliable for the detection and quantification of X. albilineans in sugarcane stalks.

Theoretical study of the geometries and decomposition energies of CO2 on Al12X: doping effect of Al12X.

The adsorption and decomposition of CO2 molecule on X-centered icosahedronal Al12X clusters (doping atom X=Al, Be, Zn, Fe, Ni, Cu, B, C, Si, P) were investigated by the DFT methods of PW91 and PWC. Adsorption energies, chemisorption energies and energy barriers of physic- and chemisorptions for CO2 were determined. It was found that the doping atoms and spin states have important influences on the Al12X geometries, electronic properties and energies of the adsorption processes. CO2 chemisorption on the Al12C cluster is energetically and kinetically unfavorable. CO2 decomposition on the metallic doping Al12X (X=Fe, Ni, Cu) clusters has relatively low energy barriers. On contrary, the barriers are large when X=B, C, Si and P. The energy barriers for CO2 chemisorption and decomposition on the Al12Fe cluster are 5.23 kJ/mol and 38.53 kJ/mol, respectively. These values are the lowest among all the clusters being discussed. The adsorption and decomposition of CO2 on the Al12X cluster can be tuned by X doping.

Adsorption of carbon dioxide on Al12X clusters studied by density functional theory: effect of charge and doping.

The adsorption of a CO2 molecule on neutral and charged X-centered icosahedron Al12X(±z) clusters (X = Al, Be, Zn, Ni, Cu, B, P; z = 0, 1) was investigated by the density functional PW91 and PWC methods. Optimized configurations corresponding to physisorption and chemisorption of CO2 were identified. The adsorption energies, activation barriers, and binding energies involving both the physisorption (Al12X(±z)·CO2-I) and chemisorption (Al12X(±z)·CO2-II) for CO2 were determined. The chemisorption of a CO2 molecule on the Al12X clusters (X is a metallic doping element) requires relatively low activation barriers. The lowest barrier was found to be with the Al12Be cluster. For the Al12X(-) clusters, the barriers are all higher than those of the neutral analogues. For the Al12X(+) clusters, two corresponding configurations are linked by a low-energy barrier, and CO2 molecule chemisorption on the Al12Be(+) cluster has the lowest barrier. The adsorption energies are larger than the energy barriers, which facilitates the chemisorption. The results show that carbon dioxide adsorbed on the Al12X(±z) clusters can be tuned by controllable X doping and the total number of valence electrons and suggest the potential application of Al12X(±z) nanostructures for carbon dioxide capture and activation.

DFT studies on doping effect of Al12X: adsorption and dissociation of H2O on Al12X clusters.

The adsorption and reaction of H2O molecule on neutral X-centered icosahedronal Al12X clusters (X = Al, Mg, Zn, Ga, Ni, Fe, B, C, Si, P) were investigated by PW91, PBE, and PWC methods. Reaction energies and reaction barriers were determined. The spin states and the doped atoms have important influences on the Al12X geometries, density, electronic properties, and energy density of reaction between Al12X with a single H2O molecule. The energies of the neutral X-centered Al12X are lower than that of surface X-replaced Al12X with the exception of Al12Mg. The H2O dissociation on the Al12X (X = Mg, Zn, Ga, Ni, Fe) clusters have relatively low activation barriers, but large activation barriers for Al12X (X = B, C, Si, P). The activation barrier of water dissociation on the singlet Al12Fe cluster is the lowest, whereas the highest barrier is with the Al12C. The reaction of H2O with Al12Fe is the most exothermic. The center-Fe atom can move out to the surface after the adsorption and dissociation of H2O with an energy barrier of 172 kJ/mol. The results showed that the water dissociation on the Al12X cluster can be tuned by controllable X doping.

DFT studies of the adsorption and dissociation of H2O on the Al13 cluster: origins of this reactivity and the mechanism for H2 release.

A theoretical study of the chemisorption and dissociation pathways of water on the Al13 cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculations revealed that the H2O molecule is easily adsorbed onto the Al13 surface, forming adlayers. The dissociation of the first H2O molecule from the bimolecular H2O structure via the Grotthuss mechanism is the most kinetically favorable among the five potential pathways for O-H bond breaking. The elimination of H2 in the reaction of an H2O molecule with a hydrogen atom on the Al cluster via the Eley-Rideal mechanism has a lower activation barrier than the elimination of H2 in the reaction of two adsorbed H atoms or the reaction of OH and H. Following the adsorption and dissociation of H2O, the structure of Al13 is distorted to varying degrees.

Synthesis, characteristic and theoretical investigation of the structure, electronic properties and second-order nonlinearity of salicylaldehyde Schiff base and their derivatives.

A series of asymmetric donor-acceptor substituted salen-type Schiff-bases have been synthesized and their structures, electronic properties and second order nonlinearities were investigated by DFT methods. In order to verify the stable of these Schiff-base derivates, the IR spectrum of these Schiff-base derivates were calculated, the result showed that these compounds are stable. The results of TD-DFT calculation indicate that the derivatives with the electron-donating group (CH3, OCH3 or N(C2H5)2) have a red shift absorption compared to derivatives with the electron-withdrawing group (NO2). The analysis of MOS indicates that the CN group has contribution to the LUMO orbital while the groups of OCH3, N(C2H5)2 and NO2 have contribution to the HOMO orbital. OCH3, N(C2H5)2 as electron rich groups, made the derivates have a larger first static hyperpolarizability. However, the compound (II) with a NO2 substituent, also has a large first static hyperpolarizability. This is probably because of the special transition model, namely the values of two oscillator strength f (fHOMO-1-LUMO=0.405, fHOMO-LUMO=0.321) are almost equal. In order to understand the influence of the energy gap (ΔE) between the HOMO and the LUMO orbitals on the first static hyperpolarizability, we calculated the energy gap (ΔE) of all Schiff-base compounds. The results show that the smaller the HOMO-LUMO energy gap is, the larger the first static hyperpolarizability is.

[Function of getting rid of cores of Cornus officinalis Sieb. et Zucc. and studies on method of processing in producing area].

OBJECTIVE: To gain a clear idea on function of getting fid of cores of Cornus officinalis Sieb. et Zucc. and elect a suitable processing method and technics of Crnus officinalis Sieb. et Zucc. in producing area. METHODS: The contents of loganin and morroniside were determined in the cores and sarocarp of Cornus officinalis Sieb. et Zucc.; Using pathogonal method, the methods which Cornus officinalis sieb. et Zuee. were warmed or poached were isolated by determining quantitively loganin from Cornus officinalis Sieb. et Zucc. by HPLC. RESULTS: There was a bit loganin and morroniside in the cores of Cornus officinalis Sieb. et Zuecc.; There were three aspects that were marked influence to extracted account of loganin which were hot temperature of poach, adding water and time of warming. The best suitable extracting technology was warmed in 60 degrees C by 10 min and then getted rid of cores. CONCLUSION: Clearing the non-medicinal positon is the function of getting rid of cores of Cornus officinalis Sieb. et Zucc. and warming is better than poach.