Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct f lower color

The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence between two parental species with different f lower color widely used for azalea breeding.Gapless genome assembly was generated for the yellow-f lowered azalea,Rhododendron molle.Comparative genomics found recent proliferation of long terminal repeat retrotransposons(LTR-RTs),especially Gypsy,has resulted in a 125 Mb(19%)genome size increase in species-specific regions,and a significant amount of dispersed gene duplicates(13402)and pseudogenes(17437).Metabolomic assessment revealed that yellow f lower coloration is attributed to the dynamic changes of carotenoids/f lavonols biosynthesis and chlorophyll degradation.Time-ordered gene co-expression networks(TO-GCNs)and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct f lower pigmentation.B3 and ERF TFs were found dominating the gene regulation of carotenoids/f lavonols characterized pigmentation in R.molle,while WRKY,ERF,WD40,C2H2,and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-f lowered R simsii.This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization

Water caltrop(Trapa spp.,Lythraceae)is a traditional but currently underutilized non-cereal crop.Here,we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa.natans(4x,AABB),i.e.,diploid T.natans(2x,AA)and Trapa incisa(2x,BB).In conjunction with four published(sub)genomes of Trapa,we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element(TE)library to develop Trapa genomic resources.The pangenome displayed substantial gene-content variationwith dispensable and private gene clusters occupying a large proportion(51.95%)of the total cluster sets in the six(sub)genomes.Genotyping of presence-absence variation(PAVs)identified 40453 PAVs associated with 2570 genes specific to A-or B-lineages,of which 1428were differentially expressed,andwere enriched in organ development process,organic substancemetabolic process and response to stimulus.Comparative genome analyses showed that the allotetraploid T.natans underwent asymmetric subgenome divergence,with the B-subgenome being more dominant than the A-subgenome.Multiple factors,including PAVs,asymmetrical amplification of TEs,homeologous exchanges(HEs),and homeolog expression divergence,together affected genome evolution after polyploidization.Overall,this study sheds lights on the genome architecture and evolution of Trapa,and facilitates its functional genomic studies and breeding program.

Evaluation of Genetic Divergence in Various Potato Genotypes Grown in Bangladesh through Different Traits Assessment

The goal of the study was to quantify the genetic diversity of different potato varieties. Five groups were named to classify the 25 genres of potatoes as: Cluster I (Lalpakri, Diamond), Cluster II (Hagrai, Green Mountain, G.M.O., Elvera), Cluster III (Atlantic, Shepody, Raja, Fundy, Multa, Granulla, Shibilati, Japanese Red), Cluster IV (Atlas, Brondy, Yucon Gold, Monona, Petrones, Cheroki), and Cluster V (Calwhite, Prelude, Allblue, Russet, Burbank, TPS-67). The highest and lowest genotypes are found in Clusters III and I, respectively. The two groups’ maximum inter-cluster distance (the cluster’s distance between them) demonstrates the enormous diversity between Clusters II & III. Cluster III had the greatest intra-cluster distance (distance within a set), whereas Cluster V had the smallest. In most cases, the distance between gaps was more significant than the distance within the holes, showing greater genetic diversity between different groups’ genotypes. The highest, second highest, and third highest eigenvalues, accompanying the positive canonical values for Vectors I and II of three characteristics: average tuber weight in each plant, the tubers number in each plant, and the eyes number in each tuber, showed the most outstanding contribution to the complete difference between genotypes. Of the nine features, the smaller leaves number in each plant, the shorter plant height, the more minor genotypes, the fewer eyes per tube generated from Cluster I, the maximum height of the plants, the high-quality tubers in each plant, the tubers number in each plant, the fresh weight in each plant, and the leaf number in each plant from Cluster II could be chosen in the role of parents in this program for hybridization. Given the size of the genetic distance, the various characteristics that contribute to the overall difference, and the average population size, Hagrai, Green Mountain, O.M.G., Elvera Cluster II and Cluster I, Lalpakri, and Diamond genotypes can be regarded as parents of hybridization programs in the future. Thus, producers can get guidance to enhance genetic diversity by selecting materials from different relatives and reducing their vulnerability to diseases and climate change.

Image reconstruction for cone-beam computed tomography using total p-variation plus Kullback-Leibler data divergence

Accurate reconstruction from a reduced data set is highly essential for computed tomography in fast and/or low dose imaging applications. Conventional total variation（TV）-based algorithms apply the L1 norm-based penalties, which are not as efficient as Lp（0〈p〈1） quasi-norm-based penalties. TV with a p-th power-based norm can serve as a feasible alternative of the conventional TV, which is referred to as total p-variation（TpV）. This paper proposes a TpV-based reconstruction model and develops an efficient algorithm. The total p-variation and Kullback-Leibler（KL） data divergence, which has better noise suppression capability compared with the often-used quadratic term, are combined to build the reconstruction model. The proposed algorithm is derived by the alternating direction method（ADM） which offers a stable, efficient, and easily coded implementation. We apply the proposed method in the reconstructions from very few views of projections（7 views evenly acquired within 180°）. The images reconstructed by the new method show clearer edges and higher numerical accuracy than the conventional TV method. Both the simulations and real CT data experiments indicate that the proposed method may be promising for practical applications.

Model-Free Ultra-High-Dimensional Feature Screening for Multi-Classified Response Data Based on Weighted Jensen-Shannon Divergence

In ultra-high-dimensional data, it is common for the response variable to be multi-classified. Therefore, this paper proposes a model-free screening method for variables whose response variable is multi-classified from the point of view of introducing Jensen-Shannon divergence to measure the importance of covariates. The idea of the method is to calculate the Jensen-Shannon divergence between the conditional probability distribution of the covariates on a given response variable and the unconditional probability distribution of the covariates, and then use the probabilities of the response variables as weights to calculate the weighted Jensen-Shannon divergence, where a larger weighted Jensen-Shannon divergence means that the covariates are more important. Additionally, we also investigated an adapted version of the method, which is to measure the relationship between the covariates and the response variable using the weighted Jensen-Shannon divergence adjusted by the logarithmic factor of the number of categories when the number of categories in each covariate varies. Then, through both theoretical and simulation experiments, it was demonstrated that the proposed methods have sure screening and ranking consistency properties. Finally, the results from simulation and real-dataset experiments show that in feature screening, the proposed methods investigated are robust in performance and faster in computational speed compared with an existing method.

Study of beam divergence and thrust vector eccentricity characteristics of the Hall thruster based on dual Faraday probe array planes and its applications

The accurate knowledge of the thrust vector eccentricity and beam divergence characteristics of Hall thrusters are of significant engineering value for the beneficial integration and successful application of Hall thrusters on spacecraft.For the characteristics of the plume bipolar diffusion due to the annular discharge channel of the Hall thruster,a Gaussian-fitted method for thrust vector deviation angle and beam divergence of Hall thrusters based on dual Faraday probe array planes was proposed in respect of the Hall thruster beam characteristics.The results show that the ratios of the deviation between the maximum and minimum values of the beam divergence angle and the thrust vector eccentricity angle using a Gaussian fit to the optimized Faraday probe dual plane to the mean value are 1.4%and 11.5%,respectively.The optimized thrust vector eccentricity angle obtained has been substantially improved,by approximately 20%.The beam divergence angle calculated using a Gaussian fitting to the optimized Faraday probe dual plane is approximately identical to the non-optimized one.The beam divergence and thrust vector eccentricity angles for different anode mass flow rates were obtained by averaging the beam divergence and thrust vector eccentricity angles calculated by the dual-plane,Gaussian-fitted ion current density method for different cross-sections.The study not only allows for an immediate and effective tool for determining the design of thrust vector adjustment mechanisms of spacecraft with different power Hall thrusters but also for characterizing the 3D spatial distribution of the Hall thruster plume.

Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time

The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity(PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America(EA-ENA disjuncts) and their associated factors remain unknown.Here we investigated the standardized effect size of PD(SES-PD),PBD,and potentially associated factors in 11natural mixed forest sites(five in EA and six in ENA) where abundant EA-ENA disjuncts occur.We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale(1.96vs-1.12),even though the number of disjunct species in ENA is much lower than in EA(128 vs 263).SESPD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites.The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites.Based on the unweighted unique fraction metric(UniFrac) distance and the phylogenetic community dissimilarity,PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites.Based on the standardized effect size of mean pairwise distances(SES-MPD),nine of eleven studied sites showed a neutral community structure(-1.96 ≤SES-MPD ≤1.96).Both Pearson’s r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time.Moreover,SES-PD of the EA-ENA disjuncts was positively correlated with temperaturerelated climatic factors,although negatively correlated with mean diversification rate and community structure.By applying approaches from phylogenetics and community ecology,our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.

A test of genetic divergence of a bird existing in the Sichuan Basin and its surrounding mountain ranges

Island ecosystems,serving as natural laboratories,facilitate geographical isolation,ecological specialization,and species divergence.The Sichuan Basin,surrounded by mountain ranges,represents a typical continental island due to its marked environmental spatial heterogeneity.This heterogeneity may contribute to geographical isolation and habitat heterogeneity,resulting in genetic divergence within populations.Therefore,we used the White-browed Laughingthrush(Garrulax sannio)as a model specimen to investigate the genetic divergence in the Sichuan Basin and its surrounding mountain ranges,given its presence in various habitats within and beyond this basin.Employing a RAD-seq dataset of 140 G.sannio individuals from 17 distinct ecological zones in the Sichuan Basin and its surrounding mountain ranges,we conducted PCA,population structure analysis,phylogenetic tree construction,and gene flow analysis to comprehensively analyze G.sannio groups.Additionally,in conjunction with geographical and ecological data,we performed isolation by distance,isolation by environment,PCA,and latent factor mixed model analysis to identify factors influencing the genetic divergence among these G.sannio groups.In summary,the 17 G.sannio groups were categorized into high-elevation,medium-elevation,and lowelevation groups.Genetic divergence in G.sannio may be attributed to both geographical distance and key ecological factors,particularly elevation and key climatic variables.Notably,the high-elevation group exhibited a greater number of SNPs and selected genes associated with the key ecological factors compared to the lowelevation group.The ADCY9 gene and several associated key pathways were identified as crucial elements driving ecological adaptation(elevation and key climatic variables)in the high-elevation group.Furthermore,climate changes during the glacial cycles may have facilitated gene flow among these groups residing in the Sichuan Basin and its surrounding mountain ranges.Our findings provide evidence of genetic divergence in G.sannio influenced by the geographical distance and key ecological factors between the Sichuan Basin and its surrounding mountain ranges.These results lay the groundwork for future research on the molecular systematics of continental islands.

How Classical, Quantum-Mechanical, and Relativistic Wave and Field Equations Are Uniformly Generated by Velocity-Field Divergence Equations

We expand previously established results concerning the uniform representability of classical and relativistic gravitational field equations by means of velocity-field divergence equations by demonstrating that conservation equations for (probability) density functions give rise to velocity-field divergence equations the solutions of which generate—by way of superposition—the totality of solutions of various well-known classical and quantum-mechanical wave equations.

RIGHT MEAN FOR THEα-z BURES-WASSERSTEIN QUANTUM DIVERGENCE

The optimization problem to minimize the weighted sum ofα-z Bures-Wasserstein quantum divergences to given positive definite Hermitian matrices has been solved.We call the unique minimizer theα-z weighted right mean,which provides a new non-commutative version of generalized mean(H?lder mean).We investigate its fundamental properties,and give many interesting operator inequalities with the matrix power mean including the Cartan mean.Moreover,we verify the trace inequality with the Wasserstein mean and provide bounds for the Hadamard product of two right means.

Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species

Due to the difficulty in accurately identifying structural variants(SVs) across genomes,their impact on cisregulato ry diverge n ce of closely related species,especially fish,remains to be explored.Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes.However,the role of broad H3K4me3 domains in phenotypic divergence remains poorly understood.Siniperca chuatsi and S.scherzeri are closely related but divergent in several phenotypic traits,making them an ideal model to study cis-regulatory evolution in sister species.Here,we generated chromosome-level genomes of S.chuatsi and S.scherzeri,with assembled genome sizes of 716.35 and740.54 Mb,respectively.The evolutionary histories of S.chuatsi and S.scherzeri were studied by inferring dynamic changes in ancestral population sizes.To explore the genetic basis of adaptation in S.chuatsi and S.scherzeri,we performed gene family expansion and contraction analysis and identified positively selected genes(PSGs).To investigate the role of SVs in cis-regulatory divergence of closely related fish species,we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of S.chuatsi and S.scherzeri.Integrated analysis revealed that cis-regulatory divergence caused by SVs played an essential role in phenotypic divergence between S.chuatsi and S.scherzeri.Additionally,divergent broad H3K4me3 domains were mostly associated with cancer-related genes in S.chuatsi and S.scherzeri and contributed to their phenotypic divergence.

The Meaning of Divergence

The concept of the divergence is fundamental in electromagnetic field theory, yet they are especially difficult mathematical concepts. Understanding this concept requires strong spatial and abstract thinking. When teaching, through the graphical and quantitative methods presented herein, the significance of the divergence is displayed by a quantitative method for the first time. Through these methods, the concepts of the divergence can be grasped more easily. These explanations will be helpful for students to strengthen the understanding of this concept and has a certain reference significance.

基于随机游走模型和KL-divergence的聚类算法

聚类分析在数据挖掘领域有着广泛的应用,该文提出一个聚类新思路,它不需要任何参数的假设,只基于数据两两之间的相似性。该方法假设数据点之间存在随机游走关系,根据数据相似性构造随机游走过程的转移矩阵,当随机游走过程进入收敛期后,t阶转移矩阵揭示了数据点的分布。用迭代方法寻找最小的KL-divergence来对这些分布聚类。该方法具有严谨的概率理论基础,避免了传统算法需要参数假设、限于局部最优等不足。实验表明,该算法具有较优的聚类效果。

基于Kullback-Leiber距离粗差探测的Bayes方法

从影响分析角度,基于Kullback-Leiber距离提出了粗差探测的Bayes方法。对非等权独立观测情形,在一定先验分布下,对数据删除模型、方差膨胀模型和均值漂移模型进行了比较分析,给出3种模型相应的Kullback-Leiber距离的计算公式,建立了粗差探测的判别法则。最后将该方法应用于边角网的粗差探测,取得了较好的效果。

THE DIVERGENCE OF LAGRANGE INTERPOLATION IN EQUIDISTANT NODES

It is a classical result of Bernstein that the sequence of Lagrange interpolation polynomials to \x\ at e-qually spaced nodes in [-1.1] diverges everywhere. except at zero and the end-points. In this paper we show that the sequence of Lagrange interpolation polynomials corresponding to the functions which possess better smoothness on equidistant nodes in [-1.1] still diverges every -where in the interval except at zero and the end-points.

Tunable 3D Nanofiber Architecture of Polycaprolactone by Divergence Electrospinning for Potential Tissue Engineering Applications

The creation of biomimetic cell environments with micro and nanoscale topographical features resembling native tissues is critical for tissue engineering. To address this challenge, this study focuses on an innovative electrospinning strategy that adopts a symmetrically divergent electric field to induce rapid self-assembly of aligned polycaprolactone(PCL) nanofibers into a centimeter-scale architecture between separately grounded bevels. The 3D microstructures of the nanofiber scaffolds were characterized through a series of sectioning in both vertical and horizontal directions. PCL/collagen(type I)nanofiber scaffolds with different density gradients were incorporated in sodium alginate hydrogels and subjected to elemental analysis. Human fibroblasts were seeded onto the scaffolds and cultured for 7 days. Our studies showed that the inclination angle of the collector had significant effects on nanofiber attributes, including the mean diameter, density gradient, and alignment gradient. The fiber density and alignment at the peripheral area of the 45°-collector decreased by 21% and 55%, respectively, along the z-axis,while those of the 60°-collector decreased by 71% and 60%, respectively. By altering the geometry of the conductive areas on the collecting bevels, polyhedral and cylindrical scaffolds composed of aligned fibers were directly fabricated. By using a four-bevel collector, the nanofibers formed a matrix of microgrids with a density of 11%. The gradient of nitrogen-to-carbon ratio in the scaffold-incorporated hydrogel was consistent with the nanofiber density gradient. The scaffolds provided biophysical stimuli to facilitate cell adhesion, proliferation, and morphogenesis in 3D.

Genetic variability and divergence studies in pod and seed traits of Pongamia pinnata(L.) Pierre., accessions in Bay Islands

In this study, we assessed the variability in pod, seed traits and oil content of 24 accessions of Pongamia pinnata collected from different parts of the Andaman and Nicobar Islands, India. The experiment was conducted at the Central Agricultural Research Institute, Port Blair during 2010 to 2011. The variability studies for pod and seed traits revealed that, the accession CPT-6 collected from New Wandoor in South Andaman recorded the maximum values for eight traits viz. pod length （75.51 mm）, pod width （34.62 mm）, pod thickness （17.55 mm）, 100 pod weight （770.33 g）, seed width （21.23 mm）, 100 seed weight （377.00 g）, oil percentage （43.92%） and germination percentage （94.7%）. However, the maximum seed length （26.46 mm） was recorded from CPT 2 and the maximum pod-seed ratio was obtained from CPT 13 and CPT 4 （2.50 and 2.44 respectively）. The phenotypic and genotypic coefficients of variations were also close to each other for all traits, but the 100 pod and seed weight exhibited higher phenotypic and genotypic coefficient of variation than the other traits. Estimates of broad sense heritability ranged from 0.30 （for seed length） to 0.95 （pod length） and genetic ad- vance as percent of the mean ranged between 11.66% and 57.40% with seed length giving the lowest value and 100 pod weight giving the high- est value. Both the phenotypic and genotypic correlation between pod length, pod width, pod thickness, 100 pod weight, seed width and 100 seed weight and between pod thickness, 100 pod weight, seed width, 100 seed weight and germination percentage were found to be strong. On the basis of non hierarchical Euclidian cluster analysis, 24 accessions were grouped into six clusters. The maximum numbers of seven accessions were included in cluster VI. The maximum intra cluster distance （10.238）shown by cluster VI and the maximum inter cluster distance （17.021） between V and HI followed by III and II （15.942）. Among the six clus- ters formed the cluster III recorded maximum oil percentage, 100 pod weight, 100 seed ,weight, pod length, pod thickness, pod width, seed width and. germination percentage, while cluster V recorded maximum pod seed ratio and germination percentage. The present findings suggest that the crossing between accessions of cluster V and cluster III will result in a wide spectrum of variability in subsequent generations.

THE DIVERGENCE OF LAGRANGE INTERPOLATION FOR |x|~α(2<α<4) AT EQUIDISTANT NODES

It is a classical result of Bernstein that the sequence of Lagrange interpolation polumomials to ｜x｜ at equally spaced nodes in [-1, 1] diverges everywhere, except at zero and the end-points. In the present paper, toe prove that the sequence of Lagrange interpolation polynomials corresponding to ｜x｜^α （2 〈 α 〈 4） on equidistant nodes in [-1, 1] diverges everywhere, except at zero and the end-points.

New Evidence for Improving Omega Estimation by Explicitly Considering Horizontal Divergence

It is well known that the quasi-geostrophic （QG） omega equation with only two contributors respectively associated with vorticity advection （VA） and temperature advection is derived for midlatitude synoptic-scale systems only.Based on reliable reanalysis data,new evidence revealed by cyclonic and anticyclonic cases indicates that forecasters might sometimes experience problems by paying too much attention to the 500-hPa VA when estimating vertical motions not only in subtropical systems but also in systems meeting all the assumptions of the QG omega equation.Our investigations also showed that explicitly considering the vertical profiles of horizontal divergence could allow for better interpretation of vertical motions and weather in these real cases,suggesting that this equation might not be sufficient due to the presence of only two horizontaldivergence-related （HDR） mechanisms and the absence of other HDR mechanisms,e.g.,frictional force,mountain barriers,diabatic/adiabatic processes,and acceleration/deceleration of air flows.

Experimental Study on the Effects of Magnetic Field Configuration near the Channel Exit on the Plume Divergence of Hall Thrusters

Experimental investigations into the effects of the magnetic field configuration near the channel exit on the plume of Hall thrusters were conducted. The magnetic field configuration near the channel exit is characterized by the inclination angle between the magnetic field lines and the thruster radial direction. Different inclination angles were obtained by varying the current ratio in the coils. The plume divergence angles were measured by a dual-directed probe. The results showed that the plume divergence angle increased obviously with the increase in the magnitude of the inclination angle near the channel exit. Therefore, in order to optimize the magnetic field for reducing plume divergence, the magnitude of the inclination angle should be reduced as much as possible. It suggests that the magnetic field configuration near the channel exit is another important factor that affects plume divergence.