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1.
We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0729-7) contains supplementary material, which is available to authorized users.  相似文献   
2.
根据拟南芥CBF基因序列的保守区设计合成一对特异引物,以菠菜基因组DNA为模板,采用PCR扩增的方法扩出一条DNA特异片段并克隆到pMD18-T载体中。用PCR法和酶切分析法对克隆片段进行鉴定并进一步进行核苷酸序列分析。序列测定该片段长为423bp。OMIGA2.0软件分析结果表明,该片段的推断氨基酸序列与黑麦(AAL35759)、小麦(AAL37944)、拟南芥(AAC78646)、大麦(AAL84170)的同源性分别为33.8%、33.1%、30.8%和30%。  相似文献   
3.
4.
Pierre Stif  Paul Mathis  Tore Vnngrd 《BBA》1984,767(3):404-414
Electron transport has been studied by flash absorption and EPR spectroscopies at 10–30 K in Photosystem I particles prepared with digitonin under different redox conditions. In the presence of ascorbate, an irreversible charge separation is progressively induced at 10 K between P-700 and iron-sulfur center A by successive laser flashes, up to a maximum which corresponds to about two-thirds of the reaction centers. In these centers, heterogeneity of the rate for center A reduction is also shown. In the other third of reaction centers, the charge separation is reversible and relaxes with a t1/2 ≈ 120 μs. When the iron-sulfur centers A and B are prereduced, the 120 μs relaxation becomes the dominant process (70–80% of the reaction centers), while a slow component (t1/2 = 50–400 ms) reflecting the recombination between P-700+ and center X occurs in a minority of reaction centers (10–15%). Flash absorption and EPR experiments show that the partner of P-700+ in the 120 μs recombination is neither X nor a chlorophyll but more probably the acceptor A1 as defined by Bonnerjea and Evans (Bonnerjea, J. and Evans, M.C.W. (1982) FEBS Lett. 148, 313–316). The role of center X in low-temperature electron flow is also discussed.  相似文献   
5.
Chloroplasts isolated from fully developed spinach leaves and incubated in the presence of isopentenyl pyrophosphate were able to synthesize rapidly geranylgeranyl chlorophyll a and geranylgeraniol.The biosynthesis of the geranylgeraniol derivatives from isopentenyl pyrophosphate is a compartimentalized process. The membrane fractions (thylakoid and envelope membranes) were essentially unable to synthesize geranylgeraniol, geranylgeranyl pyrophosphate and geranylgeranyl chlorophyll a. When stromal and thylakoid fractions were combined the capacity to synthesize geranylgeranyl chlorophyll a and geranylgeraniol was restored. When stromal and envelope membrane fractions were combined the capacity to synthesize geranylgeranyl pyrophosphate and geranylgeraniol was restored. The products of the reaction were discharged inside the lipid phase of the membranes.  相似文献   
6.
Steven W. McCauley  R. H. Ruby 《BBA》1981,638(2):268-274
We have studied the delayed fluorescence in spinach chloroplasts produced 0.5 ms after each of a pair of (sub)-microsecond flashes. We observe an increase in the delayed fluorescence from the second flash relative to that produced by the first. This increase is proportional to the product of the first and second flash irradiances, appearing as an I2 dependence if both flashes are increased together. The enhancement is observable at very weak flash levels (roughly 1 photon absorbed/100 PS II centers). If the irradiance of the first flash is increased, but the irradiance of the second held constant, the delayed fluorescence from the second flash is observed to increase, but then to saturate well below the first flash irradiance at which the delayed fluorescence from the first flash itself saturates. For most experiments, the dark time between flashes was 30 ms. If the dark time is varied, the enhancement changes, reaching a half-maximal value for a dark time of approx. 300 μs. The enhancement is stopped by hydroxylamine, but not by gramicidin, valinomycin, DCMU, or mild heating. These experiments are consistent with the notion that there are two different types of Photosystem II centers if we assume that only one type is responsible for the induction we see and has an optical cross-section about 4-times the size of the other type of center.  相似文献   
7.
Summary In pot experiments with barley, mustard, leek, lettuce and spinach, and in a field experiment with 30 cultivars of barley uptakes of K, Mg, Ca, Na and N were studied at varying concentrations and activities of these cations in the soil solution.The sum of macro cations (K, Mg, Ca, Na) in meq per 100 g aerial plant parts were independent of the chemical composition of the soil solution, but dependent on plant species and on the N concentration in the plant.The ratios of mean net inflows of Mg, Ca and K into plants and corresponding cation activity ratios (aMg/aCa and ) in the soil solution were linearly related and highly correlated under conditions in which growth rate and/or rate of incorporation into new tissues constituted the rate determining step of cation uptake. Consequently, mean net inflows of K, Mg and Ca were independent of ion concentration and ion activity of K, Mg or Ca in the soil solution under the conditions of constant activity ratio.The results agree with the concept that plants have a finite cation uptake capacity, and that plants are in a equilibrium-like state with the activities of K, Mg, and Ca ions in the soil solution. The results indicate that both ratios and content of exchangeable cations should be considered in our evaluation of soil test data.  相似文献   
8.
Spinach (Spinacia oleracea L.) is considered a nitrogen (N) intensive plant with high nitrate (NO3?) accumulation in its leaves. The current study via a two-year field trial introduced an approach by combining N fertilization from different sources (e.g., ammonium nitrate; 33.5 % N, and urea; 48 % N) at different rates (180, and 360 kg N ha?1) with the foliar spraying of molybdenum (Mo) as sodium molybdate, and/or manganese (Mn) as manganese sulphate at rates of 50 and 100 mgL?1 of each or with a mixture of Mo and Mn at rates of 50 and 50 mg L?1, respectively on growth, chemical constituents, and NO3? accumulation in spinach leaves. Our findings revealed that the highest rate of N fertilization (360 kg N ha?1) significantly increased most of the measured parameters e.g., plant length, fresh and dry weight plant?1, number of leaves plant?1, leaf area plant?1, leaf pigments (chlorophyll a, b and carotenoids), nutrients (N, P, K, Fe, Mn, Zn), total soluble carbohydrates, protein content, net assimilation rate, and NO3? accumulation, but decreased leaf area ratio and relative growth rate. Moreover, plants received urea-N fertilizer gave the highest values of all previous attributes when compared with ammonium nitrate –N fertilizers, and the lowest values of NO3? accumulation. The co-fertilization of N-Mo-Mn gave the highest values in all studied attributes and the lowest NO3? accumulation. The best treatment was recorded under the treatment of 360 kg N-urea ha?1 in parallel with the combined foliar application of Mo and Mn (50 + 50 mg L?1). Our findings proposed that the co-fertilization of N-Mo-Mn could enhance spinach yield and its quality, while reducing NO3? accumulation in leaves, resulting agronomical, environmental and economic benefits.  相似文献   
9.
Two formerly-uncharacterized subunits of 9 kDa and 14 kDa were found in spinach PSI complex. The 9 kDa subunit was released upon removal of antenna chlorophyll complex, whereas the 14 kDa subunit was tightly bound to the core complex. We determined the N-terminal amino acid sequence of the 9 kDa, and an internal sequence of the 14 kDa subunit after protease treatment, since the N-terminus of the latter protein was blocked. These partial sequences suggested that both subunits are new PSI components.  相似文献   
10.
We investigated individual and combined effects of salinity, soil boron (B), silicon (Si) and salicylic acid (SA) on the activities of major antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT and ascorbate peroxidase, APX) and non-enzymatic antioxidants (AA), proline, chlorophyll, anthocyanin, H2O2 concentration, stomatal resistance (SR), lipid peroxidation (MDA), membrane permeability (MP), and the uptake of sodium (Na), chloride (Cl), boron and Si of spinach plants. In general, salinity significantly increased H2O2 and proline concentrations, antioxidant activity, membrane permeability, lipid peroxidation and SR of the spinach plants, indicating that they were stressed, whereas application of B only increased proline concentration. However, plant fresh weights did not decline with either treatment. The application of Si decreased H2O2 and increased the activity of SOD and CAT. The application of SA increased SOD activity. Neither SA nor Si had any effect on the proline concentration, or MP. However, application of Si increased chlorophyll concentration and decreased lipid peroxidation (MDA concentration). Si treatment had no effect on SR. The concentration of B in the tissues, which was strongly increased by B treatment, was decreased by NaCl. As a result of salinity, concentrations of Na+ and Cl ions were increased in the plant tissues, and application of Si slightly increased these concentrations. These results indicate that exogenous Si application increases stress tolerance of spinach, a plant that is naturally reasonably resistant to combined salinity and B toxicity, by the enhancement of antioxidant mechanisms that reduce membrane damage. Exogenous SA has a less obvious effect, although the levels of salinity and boron stress applied were not sufficient in this experiment to reduce plant fresh weight.  相似文献   
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