Shikimic acid/quinic acid hydroxy cinnamyl transferase(HCT)is one of the key enzymes in the phenylpropanoid pathway.However,the role of the HCT gene in chlorogenic acid(CGA)biosynthesis in peach fruit remains unclear....Shikimic acid/quinic acid hydroxy cinnamyl transferase(HCT)is one of the key enzymes in the phenylpropanoid pathway.However,the role of the HCT gene in chlorogenic acid(CGA)biosynthesis in peach fruit remains unclear.For this,we identified the accumulation pattern of CGA in four peach cultivars,cloned and characterized 11 PpHCT gene members,and further analyzed the expression patterns of these PpHCT genes during fruit development.The contents of CGAs in the four peach cultivars all exhibited a trend of increasing and then decreasing during the fruit growth and development.Moreover,the contents of CGAs in the peel and flesh were tissue-specific.Gene structure analysis indicated that the PpHCT genes were highly conserved,containing two exons and one intron.The protein structure analysis demonstrated that the PpHCT proteins contained two conserved motifs(HXXXD,DFGWG)and a transferase domain(PF02458),which belonged to the BAHD acyltransferase family.The cis-acting element analysis suggested that the promoters of PpHCT genes contained many light-related,hormone-related,stress-related,tissue-specific,and circadian-related elements,and they could participate in a variety of biological processes.Phylogenetic analysis showed that the HCT proteins of peach were closely related to the HCT proteins of plum and had a close evolutionary relationship.The qRT-PCR analysis indicated that the expression levels of PpHCT1 and PpHCT2 showed an opposite trend to the accumulation of CGA,whereas the expression levels of PpHCT4,PpHCT5,PpHCT7,PpHCT8,and PpHCT11 demonstrated the same trend as CGA accumulation.It was worth noting that only PpHCT4 and PpHCT5 were highly expressed in the two high-CGA cultivars but showed low levels of expression in the two low-CGA cultivars.Therefore,it was hypothesized that these two genes might be key genes to the synthesis of CGA in peach fruit.Those findings provide a theoretical basis for further study on the biological functions of the HCT gene and help to reveal the molecular mechanism of CGA.展开更多
Prunus mume Sieb.et Zucc.,P.armeniaca L.,and P.salicina L.are economically important fruit trees in temperate regions.These species are taxonomically perplexing because of shared interspecific morphological traits and...Prunus mume Sieb.et Zucc.,P.armeniaca L.,and P.salicina L.are economically important fruit trees in temperate regions.These species are taxonomically perplexing because of shared interspecific morphological traits and variation,which are mainly attributed to hybridization.The chloroplast is cytoplasmically inherited and often used for evolutionary studies.We sequenced the complete chloroplast genomes of P.mume,P.armeniaca,and P.salicina using Illumina sequencing followed by de novo assembly.The three chloroplast genomes exhibit a typical quadripartite structure with conserved genome arrangement,structure,and moderate divergence.The lengths of the genomes are 157,815,157,797,and 157,916 bp,respectively.The length of the large single-copy region(LSC)region is 86,113,86,283,and 86,122 bp,and the length of the SSC region is 18,916,18,734,and 19,028 bp;the IR region is 26,393,26,390,and 26,383 bp,respectively.Each of the three chloroplast genomes encodes 133 genes,including 94 protein-coding,31 tRNA,and eight rRNA genes.Differential gene analysis for the three species revealed that trnY-ATA is a unique gene in P.armeniaca;in contrast,the gene trnI-TAT is only present in P.mume and P.salicina,though the position of the gene in these chloroplast genomes differs.Further comparative analysis of the complete chloroplast genome sequences revealed that the ORF genes and the sequences of linked regions rps16 and atpA,atpH and atpI,trnc-GCA and psbD,ycf3 and atpB,and rpL32 and ndhD are significantly different and may be used as molecular markers in taxonomic studies.Phylogenetic evolution analysis of the three species suggests that P.mume has a closer genetic relationship to P.armeniaca than to P.salicina.展开更多
The study of cylindrically symmetric compressible fluid is interesting from both theoretical and numerical points of view. In this paper, the typical spherical sym- metry properties of the numerical schemes are discus...The study of cylindrically symmetric compressible fluid is interesting from both theoretical and numerical points of view. In this paper, the typical spherical sym- metry properties of the numerical schemes are discussed, and an area weighted scheme is extended from a Lagrangian method to an arbitrary Lagrangian and Eulerian （ALE） method. Numerical results are presented to compare three discrete configurations, i.e., the control volume scheme, the area weighted scheme, and the plane scheme with the addition of a geometrical source. The fact that the singularity arises from the geometri- cal source term in the plane scheme is illustrated. A suggestion for choosing the discrete formulation is given when the strong shock wave problems are simulated.展开更多
This paper presents a cell-centered Godunov method based on staggered data distribu-tion in Eulerian framework.The motivation is to reduce the intrinsic entropy dissipation of classical Godunov methods in the calculat...This paper presents a cell-centered Godunov method based on staggered data distribu-tion in Eulerian framework.The motivation is to reduce the intrinsic entropy dissipation of classical Godunov methods in the calculation of an isentropic or rarefaction flow.At the same time,the property of accurate shock capturing is also retained.By analyzing the factors that cause nonphysical entropy in the conventional Godunov methods,we introduce two velocities rather than a single velocity in a cell to reduce kinetic energy dissipation.A series of redistribution strategies are adopted to update subcell quantities in order to improve accuracy.Numerical examples validate that the present method can dramatically reduce nonphysical entropy increase.Mathematics subject classification:35Q35,76N15,76M12.展开更多
The carbuncle phenomenon has been regarded as a spurious solution produced by most of contact-preserving methods.The hybrid method of combining high resolution flux with more dissipative solver is an attractive attemp...The carbuncle phenomenon has been regarded as a spurious solution produced by most of contact-preserving methods.The hybrid method of combining high resolution flux with more dissipative solver is an attractive attempt to cure this kind of non-physical phenomenon.In this paper,a matrix-based stability analysis for 2-D Euler equations is performed to explore the cause of instability of numerical schemes.By combining the Roe with HLL flux in different directions and different flux components,we give an interesting explanation to the linear numerical instability.Based on such analysis,some hybrid schemes are compared to illustrate different mechanisms in controlling shock instability.Numerical experiments are presented to verify our analysis results.The conclusion is that the scheme of restricting directly instability source is more stable than other hybrid schemes.展开更多
In this note,we propose a new method to cure numerical shock instability by hybriding different numerical fluxes in the two-dimensional Euler equations.The idea of this method is to combine a”full-wave”Riemann solve...In this note,we propose a new method to cure numerical shock instability by hybriding different numerical fluxes in the two-dimensional Euler equations.The idea of this method is to combine a”full-wave”Riemann solver and a”less-wave”Riemann solver,which uses a special modified weight based on the difference in velocity vectors.It is also found that such blending does not need to be implemented in all equations of the Euler system.We point out that the proposed method is easily extended to other”full-wave”fluxes that suffer from shock instability.Some benchmark problems are presented to validate the proposed method.展开更多
A local remapping algorithm for scalar function on quadrilateral meshes is described. The remapper from a distorted grid to a rezoned grid is usually regarded as a conservative interpolation problem. The present paper...A local remapping algorithm for scalar function on quadrilateral meshes is described. The remapper from a distorted grid to a rezoned grid is usually regarded as a conservative interpolation problem. The present paper introduces a pseudo time to transform the interpolation into an initial value problem on a moving grid, and construct a moving mesh method to solve it. The new feature of the algorithm is the introduction of multi- point information on each edge, which leads to the numerical flux consistent with grid node motion. During the procedure of deriving scheme, we illustrate a framework about how the algorithms on a rectangular mesh are easily generated to those on a moving mesh. The basic ideas include： （i） introducing coordinate transformation, which maps the irregular domain in physical space to a perfectly regular computational domain, and （ii） deriving finite volume methods in the physical domain, which can be viewed as a discretization of the transformed equation. The resulting scheme is second-order accurate, conservative and monotonicity preserving. Numerical examples are carried out to show the good performance of ore＂ schemes.展开更多
This paper presents a second-order direct arbitrary Lagrangian Eulerian(ALE)method for compressible flow in two-dimensional cylindrical geometry.This algorithm has half-face fluxes and a nodal velocity solver,which ca...This paper presents a second-order direct arbitrary Lagrangian Eulerian(ALE)method for compressible flow in two-dimensional cylindrical geometry.This algorithm has half-face fluxes and a nodal velocity solver,which can ensure the compatibility between edge fluxes and the nodal flow intrinsically.In two-dimensional cylindrical geometry,the control volume scheme and the area-weighted scheme are used respectively,which are distinguished by the discretizations for the source term in the momentum equation.The two-dimensional second-order extensions of these schemes are constructed by employing the monotone upwind scheme of conservation law(MUSCL)on unstructured meshes.Numerical results are provided to assess the robustness and accuracy of these new schemes.展开更多
基金supported by the funds of the Natural Science Foundation of Jiangsu Province(Grant No.BK20200278)the China Agriculture Research System(Grant No.CARS-30)+1 种基金the Species Conservation Project of Ministry of Agriculture and Rural Affair(Grant No.19210137)the National Crop Germplasm Resources Infrastructure in China(Grant No.NHGRC2021-NH16).
文摘Shikimic acid/quinic acid hydroxy cinnamyl transferase(HCT)is one of the key enzymes in the phenylpropanoid pathway.However,the role of the HCT gene in chlorogenic acid(CGA)biosynthesis in peach fruit remains unclear.For this,we identified the accumulation pattern of CGA in four peach cultivars,cloned and characterized 11 PpHCT gene members,and further analyzed the expression patterns of these PpHCT genes during fruit development.The contents of CGAs in the four peach cultivars all exhibited a trend of increasing and then decreasing during the fruit growth and development.Moreover,the contents of CGAs in the peel and flesh were tissue-specific.Gene structure analysis indicated that the PpHCT genes were highly conserved,containing two exons and one intron.The protein structure analysis demonstrated that the PpHCT proteins contained two conserved motifs(HXXXD,DFGWG)and a transferase domain(PF02458),which belonged to the BAHD acyltransferase family.The cis-acting element analysis suggested that the promoters of PpHCT genes contained many light-related,hormone-related,stress-related,tissue-specific,and circadian-related elements,and they could participate in a variety of biological processes.Phylogenetic analysis showed that the HCT proteins of peach were closely related to the HCT proteins of plum and had a close evolutionary relationship.The qRT-PCR analysis indicated that the expression levels of PpHCT1 and PpHCT2 showed an opposite trend to the accumulation of CGA,whereas the expression levels of PpHCT4,PpHCT5,PpHCT7,PpHCT8,and PpHCT11 demonstrated the same trend as CGA accumulation.It was worth noting that only PpHCT4 and PpHCT5 were highly expressed in the two high-CGA cultivars but showed low levels of expression in the two low-CGA cultivars.Therefore,it was hypothesized that these two genes might be key genes to the synthesis of CGA in peach fruit.Those findings provide a theoretical basis for further study on the biological functions of the HCT gene and help to reveal the molecular mechanism of CGA.
文摘Prunus mume Sieb.et Zucc.,P.armeniaca L.,and P.salicina L.are economically important fruit trees in temperate regions.These species are taxonomically perplexing because of shared interspecific morphological traits and variation,which are mainly attributed to hybridization.The chloroplast is cytoplasmically inherited and often used for evolutionary studies.We sequenced the complete chloroplast genomes of P.mume,P.armeniaca,and P.salicina using Illumina sequencing followed by de novo assembly.The three chloroplast genomes exhibit a typical quadripartite structure with conserved genome arrangement,structure,and moderate divergence.The lengths of the genomes are 157,815,157,797,and 157,916 bp,respectively.The length of the large single-copy region(LSC)region is 86,113,86,283,and 86,122 bp,and the length of the SSC region is 18,916,18,734,and 19,028 bp;the IR region is 26,393,26,390,and 26,383 bp,respectively.Each of the three chloroplast genomes encodes 133 genes,including 94 protein-coding,31 tRNA,and eight rRNA genes.Differential gene analysis for the three species revealed that trnY-ATA is a unique gene in P.armeniaca;in contrast,the gene trnI-TAT is only present in P.mume and P.salicina,though the position of the gene in these chloroplast genomes differs.Further comparative analysis of the complete chloroplast genome sequences revealed that the ORF genes and the sequences of linked regions rps16 and atpA,atpH and atpI,trnc-GCA and psbD,ycf3 and atpB,and rpL32 and ndhD are significantly different and may be used as molecular markers in taxonomic studies.Phylogenetic evolution analysis of the three species suggests that P.mume has a closer genetic relationship to P.armeniaca than to P.salicina.
基金Project supported by the National Natural Science Foundation of China(Nos.11471048 and U1630249)the Foundation of Chinese Academy of Engineering Physics(No.2014A0202010)the Foundation of Laboratory of Computational Physics(No.9140C690202140C69293)
文摘The study of cylindrically symmetric compressible fluid is interesting from both theoretical and numerical points of view. In this paper, the typical spherical sym- metry properties of the numerical schemes are discussed, and an area weighted scheme is extended from a Lagrangian method to an arbitrary Lagrangian and Eulerian （ALE） method. Numerical results are presented to compare three discrete configurations, i.e., the control volume scheme, the area weighted scheme, and the plane scheme with the addition of a geometrical source. The fact that the singularity arises from the geometri- cal source term in the plane scheme is illustrated. A suggestion for choosing the discrete formulation is given when the strong shock wave problems are simulated.
基金supported by the National Natural Science Foundation of China(Grant Nos.11971071,12302377)by the Foundation of LCP(Grant No.6142A05220201)by the China Postdoctoral Science Foundation(Grant No.2022M722185).
文摘This paper presents a cell-centered Godunov method based on staggered data distribu-tion in Eulerian framework.The motivation is to reduce the intrinsic entropy dissipation of classical Godunov methods in the calculation of an isentropic or rarefaction flow.At the same time,the property of accurate shock capturing is also retained.By analyzing the factors that cause nonphysical entropy in the conventional Godunov methods,we introduce two velocities rather than a single velocity in a cell to reduce kinetic energy dissipation.A series of redistribution strategies are adopted to update subcell quantities in order to improve accuracy.Numerical examples validate that the present method can dramatically reduce nonphysical entropy increase.Mathematics subject classification:35Q35,76N15,76M12.
基金supported by the National Natural Science Foundation of China(11071025)the Foundation of CAEP(2010A0202010)the Foundation of National Key Laboratory of Science and Technology Computation Physics and the Defense Industrial Technology Development Program(B1520110011).
文摘The carbuncle phenomenon has been regarded as a spurious solution produced by most of contact-preserving methods.The hybrid method of combining high resolution flux with more dissipative solver is an attractive attempt to cure this kind of non-physical phenomenon.In this paper,a matrix-based stability analysis for 2-D Euler equations is performed to explore the cause of instability of numerical schemes.By combining the Roe with HLL flux in different directions and different flux components,we give an interesting explanation to the linear numerical instability.Based on such analysis,some hybrid schemes are compared to illustrate different mechanisms in controlling shock instability.Numerical experiments are presented to verify our analysis results.The conclusion is that the scheme of restricting directly instability source is more stable than other hybrid schemes.
基金supported in part by the National Natural Science Foundation of China under(Grant No.10871029)foundation of LCP.
文摘In this note,we propose a new method to cure numerical shock instability by hybriding different numerical fluxes in the two-dimensional Euler equations.The idea of this method is to combine a”full-wave”Riemann solver and a”less-wave”Riemann solver,which uses a special modified weight based on the difference in velocity vectors.It is also found that such blending does not need to be implemented in all equations of the Euler system.We point out that the proposed method is easily extended to other”full-wave”fluxes that suffer from shock instability.Some benchmark problems are presented to validate the proposed method.
文摘A local remapping algorithm for scalar function on quadrilateral meshes is described. The remapper from a distorted grid to a rezoned grid is usually regarded as a conservative interpolation problem. The present paper introduces a pseudo time to transform the interpolation into an initial value problem on a moving grid, and construct a moving mesh method to solve it. The new feature of the algorithm is the introduction of multi- point information on each edge, which leads to the numerical flux consistent with grid node motion. During the procedure of deriving scheme, we illustrate a framework about how the algorithms on a rectangular mesh are easily generated to those on a moving mesh. The basic ideas include： （i） introducing coordinate transformation, which maps the irregular domain in physical space to a perfectly regular computational domain, and （ii） deriving finite volume methods in the physical domain, which can be viewed as a discretization of the transformed equation. The resulting scheme is second-order accurate, conservative and monotonicity preserving. Numerical examples are carried out to show the good performance of ore＂ schemes.
基金Project supported by the National Natural Science Foundation of China(U1630249,11971071,11971069,11871113)the Science Challenge Project(JCKY2016212A502)the Foundation of Laboratory of Computation Physics.
文摘This paper presents a second-order direct arbitrary Lagrangian Eulerian(ALE)method for compressible flow in two-dimensional cylindrical geometry.This algorithm has half-face fluxes and a nodal velocity solver,which can ensure the compatibility between edge fluxes and the nodal flow intrinsically.In two-dimensional cylindrical geometry,the control volume scheme and the area-weighted scheme are used respectively,which are distinguished by the discretizations for the source term in the momentum equation.The two-dimensional second-order extensions of these schemes are constructed by employing the monotone upwind scheme of conservation law(MUSCL)on unstructured meshes.Numerical results are provided to assess the robustness and accuracy of these new schemes.
