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.

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.

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.

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.

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.

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.

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.

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.

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.

知识状态集合准确界定的意义

教育认知诊断基于被试的作答反应估计其知识状态从而进行分类.尽管给定属性及其层级关系,其知识状态集合是唯一的,但对此并未形成共识.如有的软件包认为同一属性层级关系可对应2种不同的知识状态集合;有的研究仅仅给出属性及其层级关系的知识状态集合的真子集.针对这些情况,该文从理论上和应用上进行了分析,并给出修正的建议.

陕西三次强致灾性初夏区域性暴雨动力诊断对比分析

利用常规气象观测资料和0.25°×0.25°逐小时ERA5再分析资料,对综合评价强度指数300以上的三次陕西初夏区域性暴雨过程从水汽、动力垂直结构上进行对比分析。结果表明:①强致灾性初夏区域性暴雨发生前,中高层水汽输送来自西南气流,低层来自偏东气流,低层水汽辐合发展加强,动力强迫主要表现为700 hPa以下正涡度区发展加强并向高层延伸,对应200 hPa附近出现强负涡度中心;②暴雨开始后,低层偏东水汽输送在暴雨过程中会发生变化,水汽辐合持续加强并向高层持续输送,散度场出现低层强辐合、高层辐散的结构,而关中有双重辐合-辐散特殊结构,且正涡度区继续向高层延伸、动力抬升促使上升运动延伸至400 hPa及以上;③初夏暴雨陕南动力强迫相比关中较弱,但水汽输送、水汽含量比关中好,降水效率更高、降水总量更大。

基于EDA统计图量化的桥梁动态监测数据质量评估

探索性数据分析统计图在桥梁健康监测动态数据质量评估中已有广泛应用。为了减少人工观察统计图的主观性,通过近似度量方法实现统计图的量化分析,得到多个指标对监测数据进行快速质量评估。在运营环境激励作用下,桥梁结构动力响应具有短时线性平稳性,近似服从正态分布。以某大跨斜拉桥振动数据为研究对象,首先,绘制样本数据直方图和Q-Q图,通过观察数据分布特征预先判断数据质量,确定优、良和差3个等级。然后,分别通过KL散度和余弦相似度2种近似度量方法对样本数据直方图和Q-Q图进行量化,得到数据服从正态分布程度的指标;通过箱线图检测样本数据全局异常点,得到正常数据占比;统计分析得到量化值和先验质量等级的对应关系,确定以直方图KL散度和余弦相似度为主、以箱线图正常数据占比为辅的数据质量评估标准。最后,取部分数据为验证集,进一步验证所提方法各个指标的合理性,并给出该方法在实际工程上的应用结果。

计及表面残余应力的旋转凸凹型纳米圆板失稳分析

根据纳米材料表面残余应力和弹性板小挠度理论,建立旋转凸凹型纳米圆板横向振动微分方程,采用微分求积法得到不同条件下凸凹型纳米圆板的无量纲复频率随无量纲角速度和无量纲表面残余应力参数变化情况。研究结果显示:在周边固支和简支条件下,旋转凸凹型纳米圆板均发生第1阶发散失稳现象。在其他条件一定的情况下,周边固支凹型纳米圆板的临界失稳角速度小于凸型纳米圆板,周边简支凹型纳米圆板的临界失稳角速度大于凸型纳米圆板。临界失稳角速度随着表面残余应力的增加而增大,临界表面残余应力随着无量纲角速度的增加而增大。

时空矢量场下人群活动聚散模式提取与分析

由于传统方法缺乏顾及人群在区域间的动态流动而无法反映人群在未来(下一时刻)的活动聚散趋势,因此,文中借助时空矢量场来建模人群活动的趋向性,通过矢量场理论中的散度算子来定量计算人群活动聚散强度,将人群活动聚散模式提取问题转化为时间序列聚类问题识别出主要聚散模式。在海口市滴滴出行数据集上进行实验,选取角度偏态系数证明了主体方向计算方法的有效性,提取出了4种主要人群活动聚散模式,并结合POI类型的分布情况对4种模式进行了语义解释,为探索人类移动性提供研究思路和方法支持。

基于KL散度距离处理风电不确定性的负荷恢复分布鲁棒优化

在构建以新能源为主体的新型电力系统的背景下,在恢复控制过程中积极利用新能源并充分应对其对运行安全带来的潜在风险对于减小停电损失具有重要意义。首先,为了表征风电出力的不确定性,采用KL散度(Kullback-Leibler)距离作为筛选极端风电出力场景的控制条件,并据此构建模糊集作为风电出力典型场景。在满足相关运行安全约束的前提下,建立了以最大化加权负荷恢复量为优化目标的分布鲁棒优化模型以制定计及风电的负荷恢复方案。经松弛处理和对偶转换所得到的混合整数二阶锥模型可调用商业求解器求解。以接入规模风电场的IEEE 10机39母线系统为例进行仿真,结果表明:相比于传统的鲁棒优化方法,该方法降低了优化结果的保守性,有助于加快负荷恢复,减小停电损失。

情感分歧对社交媒体中信息再传播的影响——以微博为例

[研究目的]社交媒体中信息的再传播是目前主流传播方式之一,研究情感特征对社交媒体中信息再传播的作用,揭示情感信息影响社交媒体中信息再传播的机制,对于科学引导网络舆论、维持健康网络环境具有重要意义。[研究方法]基于认知失调理论,引入情感分歧特征进行情感分析,以社交媒体中帖子的转发数与评论数作为信息再传播效果的衡量指标,构建了情感分歧与情感倾向影响信息再传播的理论模型,并使用微博平台上的数据,对模型进行验证。[研究结论]通过对回归模型结果分析,情感分歧能够显著正向影响社交媒体信息再传播,促进帖子的转发与评论;正面情感倾向性能够显著促进帖子的转发效果,对帖子的评论数影响效果并不显著;帖子内容的情感倾向性能够调节帖子内容中的情感分歧对帖子转发的影响,而评论情感倾向能够调节评论内容中的情感分歧对帖子评论数的影响。

变截面半圆通道内超临界二氧化碳热工水力性能研究

建立了不同半圆通道的数学和物理模型,并通过与实验数据的比较,验证了所建立模型的准确性。研究了超临界二氧化碳(S-CO_(2))在等截面半圆通道、渐扩型和渐缩型通道内的热工水力换热性能,并分析了不同通道和压力对S-CO_(2)在变截面半圆通道内的热工水力性能的影响。结果表明:相较于均匀截面半圆通道,渐扩型通道恶化传热,渐缩型通道强化传热;入口和出口半径比为1.0:0.5的渐缩型半圆通道的总体换热系数最大提升了39.93%,流动传热综合性能评价因子PEC最大为1.346;当压力越靠近临界压力或热通量较低时,传热性能越高。最后,从场协同性和湍动能分布的角度解释了渐缩型变截面通道强化传热的原因。研究结果可为S-CO_(2)循环系统冷却器的设计与优化提供新的思路和理论指导。

k-Bertrand判别法

正项级数的敛散性判别法中比较精细的有Raabe判别法、Gauss判别法和Bertrand判别法.在上述方法的基础上,给出了Raabe判别法、Gauss判别法和Bertrand判别法推广的统一形式,包括非极限形式、上、下极限形式以及极限形式,称之为k-Bertrand判别法.