Genome Sequence Data of Leptosphaerulina arachidicola, a Causal Agent of Peanut Scorch Spot in China.

Peanut scorch spot caused by Leptosphaerulina arachidicola is one of the most severe leaf diseases of peanut that causes significant yield loss. Here, we report the first high-quality genome sequence of L. arachidicola JB313 isolated from an infected peanut leaf in China. The genome size is 47.66 Mb, consisting of 65 scaffolds (N50 length = 1.58 Mb) with a G+C content of 49.05%. The information in this report will provide a reference genome for future studies on the peanut scorch spot pathogen in peanut.

Low sink demand caused net photosynthetic rate decrease is closely related to the irrecoverable damage of oxygen-releasing complex and electron receptor in peach trees.

Source sink balance is one of the major determinants of carbon partitioning in plants. However, its effects on photosynthesis in fruit trees are largely unknown. In this work, the effects of low sink demand on net photosynthetic rate (Pn) and chlorophyll fluorescence after fruit removal (-fruit) in peach (Prunus persica (L.) Batsch cv. 'Zaojiubao') trees were investigated. The stepwise energy flow through photosystem II (PSII) at the reaction center (RC) was analyzed with quantitative analyses of fluorescence transient, also called JIP-test. We found that Pn was significantly lower and closely correlated to the leaf stomatal conductance (Gs) of -fruit trees than that of fruit retained (+fruit) trees. Leaf temperature (Tleaf) of -fruit trees was remarkably higher than that of +fruit trees. Day-time-period assays of chlorophyll (Chl) fluorescence revealed that, in the leaves of -fruit trees, the fluorescence parameters, such as NPQ (non-photochemical quenching coefficient) and ΦD0 (maximum quantum yield of non-photochemical de-excitation), decreased in the morning and recovered to the normal level in the afternoon, whereas other parameters, such as ΦE0 (quantum yield for electron transport at t = 0), Ψ0 (probability that a trapped exciton moves an electron to QA pool), F0 (minimum fluorescence, when all PSII RCs are open) and Wk (relative variable fluorescence at 300 µs of the chlorophyll fluorescence transient), did not. These results suggest that OEC complex and QA pool were irreversibly affected by low sink demand, whereas light harvest antenna and PSII potential efficiency retained a strong ability to recover.

Site-directed mutagenesis identified the key active site residues of alcohol acyltransferase PpAAT1 responsible for aroma biosynthesis in peach fruits.

The aroma of peach fruit is predominantly determined by the accumulation of γ-decalactone and ester compounds. A previous study showed that the biosynthesis of these aroma compounds in peach fruit is catalyzed by PpAAT1, an alcohol acyltransferase. In this work, we investigated the key active site residues responsible for γ-decalactone and ester biosynthesis. A total of 14 candidate amino acid residues possibly involved in internal esterification and 9 candidate amino acid residues possibly involved in esterification of PpAAT1 were assessed via site-directed mutagenesis. Analyses of the in vitro enzyme activities of PpAAT1 and its site-directed mutant proteins (PpAAT1-SMs) with different amino acid residue mutations as well as the contents of γ-decalactone in transgenic tobacco leaves and peach fruits transiently expressing PpAAT1 and PpAAT1-SMs revealed that site-directed mutation of H165 in the conserved HxxxD motif led to lost enzymatic activity of PpAAT1 in both internal esterification and its reactions, whereas mutation of the key amino acid residue D376 led to the total loss of γ-decalactone biosynthesis activity of PpAAT1. Mutations of 9 and 7 other amino acid residues also dramatically affected the enzymatic activity of PpAAT1 in the internal esterification and esterification reactions, respectively. Our findings provide a biochemical foundation for the mechanical biosynthesis of γ-decalactone and ester compounds catalyzed by PpAAT1 in peach fruits, which could be used to guide the molecular breeding of new peach species with more favorable aromas for consumers.

Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination.

UNLABELLED: Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission. IMPORTANCE: Although horseshoe bats are the primary reservoir of SARS-related coronaviruses (SARSr-CoVs), it is still unclear how these bat viruses have evolved to cross the species barrier to infect civets and humans. Most human SARS-CoV epidemic strains contain a signature 29-nucleotide deletion in ORF8, compared to civet SARSr-CoVs, suggesting that ORF8 may be important for interspecies transmission. However, the origin of SARS-CoV ORF8 remains obscure. In particular, SARSr-Rs-BatCoVs from Chinese horseshoe bats (Rhinolophus sinicus) exhibited <40% amino acid identities to human/civet SARS-CoV in the ORF8 protein. We detected diverse alphacoronaviruses and betacoronaviruses among various bat species in Yunnan, China, including two SARSr-Rf-BatCoVs from greater horseshoe bats that possessed ORF8 proteins with exceptionally high amino acid identities to that of human/civet SARSr-CoVs. We demonstrated recombination events around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. Our findings offer insight into the evolutionary origin of SARS-CoV ORF8 protein, which was likely acquired from SARSr-CoVs of greater horseshoe bats through recombination.

RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies.

Ammonium is the main inorganic nitrogen source in paddy soil. Rice (Oryza sativa), an ammonium-preferring and -tolerant grain crop, is a valuable resource for researching ammonium-uptake mechanism and understanding the molecular networks that the plant copes with ammonium variation. To generate a broad survey of early responses affected by varied ammonium supplies in rice, RNA samples were prepared from the roots and shoots of rice plants subjected to nitrogen-free (0mM ammonium), 1mM ammonium and high ammonium (10mM ammonium) for a short period of 4h (1mM ammonium treatment as the control), respectively, and the transcripts were sequenced using the Illumina/HiSeq™ 2000 RNA sequencing (RNA-Seq) platform. By comparative analysis, 394 differentially expressed genes (DEGs) were identified in roots, among which, 143 and 251 DEGs were up- and down-regulated under nitrogen-free condition, respectively. In shoots, 468 (119 up-regulated/349 down-regulated) DEGs were found under such condition. However, with high ammonium treatment, only 63 genes (6 up-regulated/57 down-regulated) in roots and 115 genes in shoots (93 up-regulated/22 down-regulated) were differentially expressed. According to KEGG analysis, when exposed to nitrogen-free condition, DEGs participating in the carbohydrate and amino acid metabolisms were down-regulated (with 1 exception) in roots as well as in shoots, implying reduced carbohydrate and nitrogen metabolisms. Under high ammonium supply, all DEGs associated with carbohydrate and amino acid metabolisms were down-regulated in roots and to the contrary, up-regulated in shoots. Aldehyde dehydrogenase (ALDH, NAD(+)) [EC: 1.2.1.3] seemed to have played an important role in rice shoots under high ammonium condition, analysis results implicated a coordinative regulation of carbohydrate with amino acid metabolisms under nitrogen deficiency as well as the high ammonium conditions during a short period of several hours in rice. Moreover, transcripts with abundance variation might be precious gene resources in responding to different ammonium supplies in rice.

[Effect of a novel plant molluscicide "Luo-wei" against Oncomelania hupensis in plateau mountain areas].

OBJECTIVE: To evaluate the effect of a novel plant molluscicide, 4%"Luo-wei" (Tea-seed distilled saponins, TDS) against Oncomelania hupensis snails in plateau mountain areas in Yunnan Province. METHODS: The immersing and spraying experiments were carried out in the ditches and grassland of Xiaolian Administrative Village in Heqing County, Yunnan Province, to assess the molluscicidal effect of 4% TDS comparing with 50% wettable powder of niclosamide ethanolamine salt (WPN) in different environments and time. RESULTS: After immersion for 24, 48 h and 72 h, the snail death rates were 70.67%, 87.33% and 98.67% in the TDS group, whereas being 77.33%, 96.67% and 100.00% in the WPN group, respectively. The differences of the death rates between the two groups 24 h and 72 h after immersing were not statistically significant ( chi2(24h) =1.73, chi2(72h) = 2.01, both P values > 0.05). Seven days after the immersing experiments, the occurrence rate of frames with living snails and the death rate of snails were 20.00% and 93.03% in the TDS group, while those were 13.33% and 95.76% in the WPN group, and there were no significant differences of the 2 indexes between the 2 groups ( chi(2)(Occurrence rate) = 2.27, chi(2)(Death rate) = 0.94, all P values > 0.05). After spraying for 1, 3, 7 d and 15 d, in both groups, the occurrence rates of frames with living snails and the average densities of living snails gradually declined, while the death rates of snails gradually increased with the extension of time. There were no statistically significant differences of the above 3 indexes between the 2 groups (all P values > 0.05). Fifteen days after the spraying experiment, the occurrence rate of frames with living snails and the adjusted death rate of snails were 15.00% and 87.39% in the TDS group and those were 16.67% and 89.32% in the WPN group, respectively. CONCLUSION: The molluscicidal effect of TDS is satisfying in plateau mountain areas, and the molluscicide is worthy of further extension and application.

Comparative genomic analysis of gene variations of two Chinese Yersinia pestis isolates from vaccine strain EV76.

OBJECTIVE: To investigate genomic variations of two Chinese Yersinia pestis isolates that were isolated from different plague foci obtained from vaccine strain EV76 from the Yunnan province of China. METHODS: A microarray containing 12 000 probes covering the entire genome of seven Yersinia pestis and two Yersinia pseudotuberculosis strains, was used. PCR assays were performed to confirm microarray results. RESULTS: The gene variations detected included the absence of five genes related to the synthesis of betaine in both EV76 and another sequenced attenuated strain, KIM D27. Several genes related to phage-related membrane proteins were found to be absent in the Antiqua biovar Yunnan strain, 485, which was isolated from a rodent plague foci. CONCLUSION: These findings provide initial insight into the distinct strains isolated from natural foci, within their genomic context, including Yunnan Y. pestis strains. This information will be used therefore to establish subsequent comparisons of these sequences with published complete genomes of other strains.

[Preparation and identification of monoclonal antibodies against Pla protein of Yersinia pestis].

AIM: To prepare the monoclonal antibody of Pla with recombinant Pla (rPla) by hybridoma cell technology, which will lay the foundation for related research work. METHODS: Purified rPla was collected by washing repeatedly with urea, and BALB/c mice were immunized by them. Hybridoma cells were achieved by Sp2/0 cell fusion with mouse spleen cells from successfully immunized mice. Monoclonal antibody was screened by indirect ELISA and Western blots with rPla, natural crude Pla and GST respectively. RESULTS: Three strains of hybridoma cells (named 15B8, 14H4 and 19A4 respectively) which secreted stably the monoclonal antibody of Pla were obtained. Their subclasses were IgG2a and IgG1 in heavy chains and κ chains in light chains. The ELISA titers of ascites were 10(6); respectively.Three of monoclonal antibody can react with natural crude Pla tested by western blots. CONCLUSION: Monoclonal antibody of natural Pla of Yersinia pestis were successfully got, which has laid the foundation for further study of the Pla protein and development diagnosis reagent.

The xrvA gene of Xanthomonas oryzae pv. oryzae, encoding an H-NS-like protein, regulates virulence in rice.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight disease in rice, one of the most serious rice diseases. The xrvA gene from Xoo strain 1,3751 encodes a protein containing a histone-like nucleoid-structuring protein (H-NS) domain. The expression of xrvA in strain 1,3751 was enhanced in XOM2 minimal medium. Mutation of the xrvA gene of strain 1,3751 led to a significant reduction in virulence in the host plant rice, a delayed hypersensitive response in the nonhost castor-oil plant, a decrease in extracellular polysaccharide and diffusible signal factor production, and an increase in intracellular glycogen accumulation. Northern hybridization analyses revealed that the virulence-associated genes hrpG, hrpX, rpfC, rpfF, rpfG and gumB were downregulated in the xrvA mutant compared to the wild-type and complemented strains. Interestingly, increase of copy number of xrvA in the wild-type strain 1,3751 resulted in a strain showing similar phenotypes as the xrvA mutant and a reduction of the expression of gumB, hrpX, rpfC, rpfF and rpfG. These findings indicate that the xrvA gene, which is highly conserved in the sequenced strains of Xanthomonas, encodes an important regulatory factor for the virulence of Xoo.

Two New Modes of Pd-Catalyzed Domino-Tetracyclization of Bromodienynes-5-exo-trig Cyclization Wins over ß-Hydride Elimination.

Remarkable increases of molecular complexity in a single procedural step are achieved with the title reaction. Only a slight modification in the substitution pattern on the acyclic precursor 2 can change the mode of tetracyclization to either yield skeletons of type 1 or 3 exclusively.