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951.
Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species
Background
Disease resistance (R) genes from different Rosaceae species have been identified by map-based cloning for resistance breeding. However, there are few reports describing the pattern of R-gene evolution in Rosaceae species because several Rosaceae genome sequences have only recently become available.Results
Since most disease resistance genes encode NBS-LRR proteins, we performed a systematic genome-wide survey of NBS-LRR genes between five Rosaceae species, namely Fragaria vesca (strawberry), Malus × domestica (apple), Pyrus bretschneideri (pear), Prunus persica (peach) and Prunus mume (mei) which contained 144, 748, 469, 354 and 352 NBS-LRR genes, respectively. A high proportion of multi-genes and similar Ks peaks (Ks = 0.1- 0.2) of gene families in the four woody genomes were detected. A total of 385 species-specific duplicate clades were observed in the phylogenetic tree constructed using all 2067 NBS-LRR genes. High percentages of NBS-LRR genes derived from species-specific duplication were found among the five genomes (61.81% in strawberry, 66.04% in apple, 48.61% in pear, 37.01% in peach and 40.05% in mei). Furthermore, the Ks and Ka/Ks values of TIR-NBS-LRR genes (TNLs) were significantly greater than those of non-TIR-NBS-LRR genes (non-TNLs), and most of the NBS-LRRs had Ka/Ks ratios less than 1, suggesting that they were evolving under a subfunctionalization model driven by purifying selection.Conclusions
Our results indicate that recent duplications played an important role in the evolution of NBS-LRR genes in the four woody perennial Rosaceae species. Based on the phylogenetic tree produced, it could be inferred that species-specific duplication has mainly contributed to the expansion of NBS-LRR genes in the five Rosaceae species. In addition, the Ks and Ka/Ks ratios suggest that the rapidly evolved TNLs have different evolutionary patterns to adapt to different pathogens compared with non-TNL resistant genes.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1291-0) contains supplementary material, which is available to authorized users. 相似文献952.
Xiuna Wang Xiaoling Zhang Ling Liu Meichun Xiang Wenzhao Wang Xiang Sun Yongsheng Che Liangdong Guo Gang Liu Liyun Guo Chengshu Wang Wen-Bing Yin Marc Stadler Xinyu Zhang Xingzhong Liu 《BMC genomics》2015,16(1)
Background
In recent years, the genus Pestalotiopsis is receiving increasing attention, not only because of its economic impact as a plant pathogen but also as a commonly isolated endophyte which is an important source of bioactive natural products. Pestalotiopsis fici Steyaert W106-1/CGMCC3.15140 as an endophyte of tea produces numerous novel secondary metabolites, including chloropupukeananin, a derivative of chlorinated pupukeanane that is first discovered in fungi. Some of them might be important as the drug leads for future pharmaceutics.Results
Here, we report the genome sequence of the endophytic fungus of tea Pestalotiopsis fici W106-1/CGMCC3.15140. The abundant carbohydrate-active enzymes especially significantly expanding pectinases allow the fungus to utilize the limited intercellular nutrients within the host plants, suggesting adaptation of the fungus to endophytic lifestyle. The P. fici genome encodes a rich set of secondary metabolite synthesis genes, including 27 polyketide synthases (PKSs), 12 non-ribosomal peptide synthases (NRPSs), five dimethylallyl tryptophan synthases, four putative PKS-like enzymes, 15 putative NRPS-like enzymes, 15 terpenoid synthases, seven terpenoid cyclases, seven fatty-acid synthases, and five hybrids of PKS-NRPS. The majority of these core enzymes distributed into 74 secondary metabolite clusters. The putative Diels-Alderase genes have undergone expansion.Conclusion
The significant expansion of pectinase encoding genes provides essential insight in the life strategy of endophytes, and richness of gene clusters for secondary metabolites reveals high potential of natural products of endophytic fungi.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-014-1190-9) contains supplementary material, which is available to authorized users. 相似文献953.
954.
Qiongbo Hu Shuyan Liu Fei Yin Shujia Cai Guohua Zhong Shunxiang Ren 《Biocontrol Science and Technology》2011,21(2):225-234
To comprehend the diversity and potential control of soil-dwelling fungi, Isaria and Paecilomyces, against the red imported fire ant Solenopsis invicta (Hymenoptera, Formicidae), an investigation was carried out between 2004 and 2008. From 258 soil samples collected from 16 central and southern provinces and cities in China, a total of 171 isolates of the genra Isaria and Paecilomyce were isolated, and the species I. javanicus, P. marquandii and I. fumosoroseus were found more abundant than I. cateniobliquus, P. carneus, P. inflatus and P. lilacinus. Geographic differences of isolating rates were observed as well. Samples from the southern areas had higher fungal isolating rates than those from the central areas. Subsequently, 47 isolates were further tested for pathogencity against the red imported fire ant. All isolates except P115 showed certain pathogenic potential (the mean is 52.3% at 4000 conidiospores/mL) to the ant. I. javanicus was the most effective species with a mean pathogenicity of 80.6%, while pathogenicities of P. marquandii, P. gunni and I. fumosoroseus were 44, 21 and 49%, respectively. Furthermore, the more effective isolates P028 of I. javanicus and P003 of I. fumosoroseus were tested in a virulence experiment. The LD50 values of P028 and P003 against major and miner workers were determined as 412,280 and 854,451 conidiospores/cm2, respectively. Meanwhile, the LT50 values at 1000 conidiospores/cm2 were 7.1 and 6.6 d in isolate P003 and 6.8 and 6.6 d in isolate P028. 相似文献
955.
Jin L Shang L Guo S Fang Y Wen D Wang L Yin J Dong S 《Biosensors & bioelectronics》2011,26(5):1965-1969
In this work, biomolecule-stabilized Au nanoclusters were demonstrated as a novel fluorescence probe for sensitive and selective detection of glucose. The fluorescence of Au nanoclusters was found to be quenched effectively by the enzymatically generated hydrogen peroxide (H(2)O(2)). By virtue of the specific response, the present assay allowed for the selective determination of glucose in the range of 1.0×10(-5) M to 0.5×10(-3) M with a detection limit of 5.0×10(-6) M. The absorption spectroscopy, X-ray photoelectron spectroscopy (XPS) and fluorescence decay studies were then performed to discuss the quenching mechanism. In addition, we demonstrated the application of the present approach in real serum samples, which suggested its great potential for diagnostic purposes. 相似文献
956.
Two different hydrogen peroxide sensors were constructed with Ni/Al and Co/Al layered double hydroxides (LDHs) modified glassy carbon electrodes (GCE). Ni (Co)/Al-LDHs were synthesized by electrochemical method and were characterized by scanning electron microscopy (SEM) and energy dispersive spectrometry (EDS). The advantages and shortcoming of the two hydrogen peroxide sensors were described in detail. Compared to Co/Al-LDHs modified electrode, sensors fabricated by Ni/Al-LDHs showed quicker heterogeneous electron transfer rate constants (k(s)), lower detection and better reproducibility. But Co/Al-LDHs modified electrode held the advantages of wider linear range and higher sensitivity. Further more, the different catalytic redox mechanisms of hydrogen peroxide on the Ni/Al/GCE and Co/Al/GCE were firstly comparatively explored. 相似文献
957.
Tripropylamine (TPA) has different oxidation efficiency at double stranded (ds)-and single stranded (ss)-DNA-modified electrodes. Using this property, a simple but sensitive biosensor using TPA oxidation to probe the intramolecular displacement was constructed with the analysis of lysozyme as model for the first time. After the complementary ss-DNA strand of anti-lysozyme aptamer was immobilized onto gold electrode via gold-thiol bond, the incubation with the aptamer resulted in the formation of ds-DNA. Lysozyme (in 10 μL sample) binding with aptamer displaced the complementary strand because of the high affinity of lysozyme and its aptamer, corresponding to the dissociation of the ds-DNA. The modified electrode was swept in 20mM TPA solution from 0.2 to 0.95 V. The difference in oxidation current was used to quantify the content of lysozyme with a linear range from 1.0 pM to 1.1 nM. That means 10 amol or 6.0 × 10(6) lysozyme molecules can be detected. Because the signal is produced from the preconcentrated TPA at the electrode surface, the high sensitivity is achieved over the single site labelling strategy. The proposed method is simple, stable, specific, and time-saving while the complicated sample pre-treatment and the labelling to the DNA strand are avoided. The biosensor was validated by the analysis of the diluted egg white sample directly. The recovery and reproducibility were 93.3-100% and 1.4-4.2%, respectively. 相似文献
958.
The present work demonstrates a rapid, single-step and ultrasensitive label-free and signal-off electrochemical sensor for specific DNA detection with excellent discrimination ability for single-nucleotide polymorphisms, taking advantage of Exonuclease III (Exo III)-aided target recycling strategy to achieve signal amplification. Exo III has a specifical exo-deoxyribonuclease activity for duplex DNAs in the direction from 3' to 5' terminus, however its activity on the duplex DNAs with 3'-overhang and single-strand DNA is limited. In response to the specific features of Exo III, the proposed E-DNA sensor is designed such that, in the presence of target DNA, the electrode self-assembled signaling probe hybridizes with the target DNA to form a duplex in the form of a 3'-blunt end at signaling probe and a 3'-overhang end at target DNA. In this way, Exo III specifically recognizes this structure and selectively digests the signaling probe. As a result, the target DNA dissociates from the duplex and recycles to hybridize with a new signaling probe, leading to the digestion of a large amount of signaling probes gradually. A redox mediator, Ru(NH(3))(6)(3+) (RuHex) is employed to electrostatically adsorbed onto signaling probes, which is directly related to the amount and the length of the signaling probes remaining in the electrode, and provides a quantitative measure of sequence-specific DNA with the experimentally measured (not extrapolated) detection limit as low as 20 fM. Moreover, this E-DNA sensor has an excellent differentiation ability for single mismatches with fairly good stability. 相似文献
959.
The graphene nanosheets and carbon nanospheres mixture (GNS–CNS) was prepared by electrolyzing graphite rob in KNO3 solution under constant current, which was characterized by TEM, AFM, SEM, FT-IR, XRD, XPS, TGA and UV–vis. The nano-mixture can keep stable in water for more than one month. Based on this kind of mixture material, a novel electrochemical biosensing platform for glucose determination was developed. Cyclic voltammetry of glucose oxidase (GOD) immobilized on GNS–CNS/GCE exhibited a pair of well-defined quasi-reversible redox peaks at −0.488 V (Epa) and −0.509 V (Epc) by direct electron transfer between the protein and the electrode. The charge-transfer coefficient (α) was 0.51, the electron transfer rate constant was 2.64 s−1 and the surface coverage of HRP was 3.18 × 10−10 mol cm−2. The immobilized GOD could retain its bioactivity and catalyze the reduction of dissolved oxygen. The glucose biosensor has a linear range from 0.4 to 20 mM with detection limit of 0.1 mM. Moreover, the biosensor exhibits acceptable reproducibility and storage stability. The fabricated biosensor was further used to determine glucose in human plasma sample with the recoveries from 96.83% to 105.52%. Therefore, GOD/GNS–CNS/GCE could be promisingly applied to determine blood sugar concentration in the practical clinical analysis. 相似文献
960.
Qi Wang Cui Min Tingting Yan Hefang Pu Yinqiang Xin Shuangquan Zhang Lan Luo Zhimin Yin 《World journal of microbiology & biotechnology》2011,27(11):2603-2610
l-glutamine (Gln) is an important conditionally necessary amino acid in human body and potential demand in food or medicine
industry is expected. High efficiency of l-Gln production by coupling genetic engineered bacterial glutamine synthetase (GS) with yeast alcoholic fermentation system
has been developed. We report here first the application of small ubiquitin-related modifier (SUMO) fusion technology to the
expression and purification of recombinant Bacillus subtilis GS. In order to obtain GS with high Gln-forming activity, safety and low cost for food and pharmaceutics industry, 0.1% (w/v)
lactose was selected as inducer. The fusion protein was expressed in totally soluble form in E. coli, and expression was verified by SDS–PAGE and western blot analysis. The fusion protein was purified to 90% purity by nickel
nitrilo-triacetic acid (Ni–NTA) resin chromatography with a yield of 625 mg per liter fermentation culture. After the SUMO/GS
fusion protein was cleaved by the SUMO protease, the cleaved sample was reapplied to a Ni–NTA column. Finally, about 121 mg
recombinant GS was obtained from 1 l fermentation culture with no less than 96% purity. The recombinant purified GS showed
great transferase activity (23 U/mg), with 25 U recombinant GS in a 50 ml reaction system, a biosynthesis yield of 27.5 g/l l-Gln was detected by high pressure liquid chromatography (HPLC) or thin-layer chromatography. Thus, the application of SUMO
technology to the expression and purification of GS potentially could be employed for the industrial production of l-Gln. 相似文献