21 research outputs found
The Euscaphis japonica genome and the evolution of malvids
Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological
and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis
japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the
unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization
event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two
polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly
known as the c event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing
101 samples from 11 populations, we speculate that the temperature has led to the differentiation
of the evergreen and deciduous of E. japonica and the completely different population histories of these
two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of
which are involved in flower and fruit development. We found that reddening and dehiscence of the E.
japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and
revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key
genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression
patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the
evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis
for their fruit dehiscence and abscission.DATA AVAILABILITY STATEMENT : All sequences described in this manuscript have been submitted to the National Genomics Data Center (NGDC). The raw whole-genome data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005268/CRA004271, and the assembly and annotation data have been deposited at BioProject/GWH (https://bigd.big.ac.cn/gwh) under the accession codes PRJCA005268/GWHBCHS00000000. The raw transcriptomes data of E. japonica have been deposited in BioProject/GSA (https://bigd.big.ac.cn/gsa.) under the accession codes PRJCA005298/CRA004272.SUPPLEMENTARY MATERIAL 1: Supplementary Note 1. Chromosome number assessment.
Supplementary Note 2. Whole-genome duplication identification and dating.
Supplementary Note 3. Observation of E. japonica seed dispersal.
Supplementary Note 4. Determination of pentacyclic triterpene substances.
Figure S1. Cytogenetic analysis of E. japonica.
Figure S2. Genome size and heterozygosity of E. japonica estimation using 17 k-mer distribution.
Figure S3. Interchromosomal of Hi-C chromosome contact map of E. japonica genome.
Figure S4. Gene structure prediction results of E. japonica and other species.
Figure S5. Venn diagram shows gene families of malvids.
Figure S6. Phylogenetic tree constructed by chloroplast genomes from 17 species.
Figure S7. Concatenated- and ASTRAL-based phylogenetic trees.
Figure S8. Ks distribution in E. japonica.
Figure S9. Distributions of synonymous substitutions per synonymous site (Ks) of one-to-one orthologs identified between E. japonica and P. trichocarpa and V. vinifera.
Figure S10. Population structure plot.
Figure S11. Fixation index (FST) heat map among E. japonica populations.
Figure S12. Phylogenetic analysis of MADS-box genes from O. sativa, A. thaliana, E. japonica, and T. cacao.
Figure S13. Observation the fruit development.
Figure S14. Animal seed dispersal.
Figure S15. Anthocyanin biosynthesis in E. japonica fruits.
Figure S16. Carotenoid accumulation and the chlorophyll degradation in E. japonica fruits.
Figure S17. Expression profile of fruit dehiscence-related genes.
Figure S18. Phylogenetic tree of DELLA genes obtained from six malvids species.
Figure S19. Phylogenetic tree of CAD genes obtained from seven malvids species.
Figure S20. Expression pattern of fruit abscission-related genes.
Figure S21. Structure of pentacyclic triterpene compounds separated from Euscaphis.
Figure S22. Phylogenetic tree of HMGR gene in plants.
Figure S23. Phylogenetic tree of P450s gene family obtained from A. thaliana and E. japonica.SUPPLEMENTARY MATERIAL 2: Table S1. Assembled statistics of E. japonica genome.
Table S2. Evaluation of E. japonica genome assembly.
Table S3. Chromosome length of E. japonica.
Table S4. Prediction of gene structures of the E. japonica genome.
Table S5. Statistics on the function annotation of the E. japonica genome.
Table S6. Non-coding RNA annotation results of E. japonica genome.
Table S7. BUSCO assessment of the E. japonica annotated genome.
Table S8. Statistic of repeat sequence in E. japonica genome.
Table S9. Gene-clustering statistics for 17 species.
Table S10. KEGG enrichment result of unique genes families of E. japonica.
Table S11. Gene Ontology (GO) and KEGG enrichment result of significant shared by malvids species gene families.
Table S12. Gene Ontology (GO) and KEGG enrichment result of significant expansion of E. japonica gene families.
Table S13. Gene Ontology (GO) enrichment result of significant contraction of E. japonica gene families.
Table S14. Statistical sampling population information.
Table S15. Statistics population resequencing information.
Table S16. Statistical nucleotide polymorphisms in the populations.
Table S17. Candidate positive selection genes (PSGs) in the evergreen population.
Table S18. Candidate positive selection genes (PSGs) in the deciduous population.
Table S19. Gene Ontology (GO) enrichment result of significant PSGs in the evergreen population.
Table S20. List of MADS-box genes identified in E. japonica.
Table S21. Genes involved in anthocyanin biosynthesis, carotenoid biosynthesis, and chlorophyll degradation.
Table S22. Identification fruit dehiscence-related genes in E. japonica.
Table S23. Genes related to lignin synthesis that are highly expressed during pericarp dehiscence.
Table S24. Gene expression levels (FPKMs) of fruit abscission-related genes in pericarp.
Table S25. Triterpene compounds separated from Euscaphis.
Table S26. Number of putative pentacyclic triterpene-related genes in the malvids species.
Table S27. Identified pentacyclic triterpene synthesis-related genes in E. japonica genome.
Table S28. Statistical simple sequence repeat.Fund for Excellent Doctoral Dissertation of Fujian Agriculture and Forestry University, China; Fujian Provincial Department of Science E. japonica Evolution and Selection of Ornamental Medicinal Resources, China; the Project of Forestry Peak Discipline at Fujian Agriculture and Forestry University, China; the Collection, Development and Utilization of Eascaphis konlshli Germplasm Resources; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program and from Ghent University.https://onlinelibrary.wiley.com/journal/1365313xam2022BiochemistryGeneticsMicrobiology and Plant Patholog
Numerical Study on the Influence of Shaping Air Holes on Atomization Performance in Pneumatic Atomizers
In pneumatic atomizers, the shaping air holes play an important role in the spraying system. The pressure and intersection of shaping air holes are the two most important parameters in engineering. In this paper, the Euler–Lagrangian method is used to describe the two-phase spray flow. The spraying process of the pneumatic nozzle is simulated numerically, and the experiment is designed to verify this simulation. By setting different air pressures and distances between the intersection and the paint hole, target surface pressure and droplet size distribution are investigated in detail, in order to explore the relationship between shaping air holes in pneumatic nozzles and overspray. From the results of the numerical simulation, it is found that an increase in the distance between the intersection and the paint hole increases the gas velocity at the central axis of the nozzle and the central pressure of the target surface, the droplet size becomes larger, and the distribution of droplets is more concentrated on the target surface, which easily leads to overspray. With the increase in the pressure of the shaping air holes, the central pressure of the target surface decreases, and the ovality of the spraying pattern on the target surface increases
A Numerical Investigation on Droplet Bag Breakup Behavior of Polymer Solution
The deformation and breakup of a polymer solution droplet plays a key role in inkjet printing technology, tablet-coating process, and other spray processes. In this study, the bag breakup behavior of the polymer droplet is investigated numerically. The simple coupled level set and volume of fluid (S-CLSVOF) method and the adaptive mesh refinement (AMR) technique are employed in the droplet breakup cases at different Weber numbers and Ohnesorge numbers. The nature of the polymer solution is handled using Herschel–Bulkley constitutive equations to describe the shear-thinning behavior. Breakup processes, external flow fields, deformation characteristics, energy evolutions, and drag coefficients are analyzed in detail. For the bag breakup of polymer droplets, the liquid bag will form an obvious reticular structure, which is very different from the breakup of a Newtonian fluid. It is found that when the aerodynamic force is dominant, the increase of the droplet viscous force will prolong the breakup time, but has little effect on the final kinetic energy of the droplet. Moreover, considering the large deformation of the droplet in the gas flow, a new formula with the cross-diameter (Dcro) is introduced to modify the droplet drag coefficient
A multi-model based adaptive reconfiguration control scheme for an electro-hydraulic position servo system
Reliability and safety of an electro-hydraulic position servo system (EHPSS) can be greatly reduced for potential sensor and actuator faults. This paper proposes a novel reconfiguration control (RC) scheme that combines multi-model and adaptive control to compensate for the adverse effects. Such a design includes several fixed models, one adaptive model, and one reinitialized adaptive model. Each of the models has its own independent controller that is based on a complete parametrization of the corresponding fault. A proper switching mechanism is set up to select the most appropriate controller to control the current plant. The system output can track the reference model asymptotically using the proposed method. Simulation results validate robustness and effectiveness of the proposed scheme. The main contribution is a reconfiguration control method that can handle component faults and maintain the acceptable performance of the EHPSS
A Novel Epidemic Model Base on Pulse Charging in Wireless Rechargeable Sensor Networks
As wireless rechargeable sensor networks (WRSNs) are gradually being widely accepted and recognized, the security issues of WRSNs have also become the focus of research discussion. In the existing WRSNs research, few people introduced the idea of pulse charging. Taking into account the utilization rate of nodes’ energy, this paper proposes a novel pulse infectious disease model (SIALS-P), which is composed of susceptible, infected, anti-malware and low-energy susceptible states under pulse charging, to deal with the security issues of WRSNs. In each periodic pulse point, some parts of low energy states (LS nodes, LI nodes) will be converted into the normal energy states (S nodes, I nodes) to control the number of susceptible nodes and infected nodes. This paper first analyzes the local stability of the SIALS-P model by Floquet theory. Then, a suitable comparison system is given by comparing theorem to analyze the stability of malware-free T-period solution and the persistence of malware transmission. Additionally, the optimal control of the proposed model is analyzed. Finally, the comparative simulation analysis regarding the proposed model, the non-charging model and the continuous charging model is given, and the effects of parameters on the basic reproduction number of the three models are shown. Meanwhile, the sensitivity of each parameter and the optimal control theory is further verified
Adaptive Fuzzy Active-Disturbance Rejection Control-Based Reconfiguration Controller Design for Aircraft Anti-Skid Braking System
The aircraft anti-skid braking system (AABS) is an essential aero electromechanical system to ensure safe take-off, landing, and taxiing of aircraft. In addition to the strong nonlinearity, strong coupling, and time-varying parameters in aircraft dynamics, the faults of actuators, sensors, and other components can also seriously affect the safety and reliability of AABS. In this paper, a reconfiguration controller-based adaptive fuzzy active-disturbance rejection control (AFADRC) is proposed for AABS to meet increased performance demands in fault-perturbed conditions as well as those concerning reliability and safety requirements. The developed controller takes component faults, external disturbance, and measurement noise as the total perturbations, which are estimated by an adaptive extended state observer (AESO). The nonlinear state error feedback (NLSEF) combined with fuzzy logic can compensate for the adverse effects and ensure that the faulty AABS maintains acceptable performance. Numerical simulations are carried out in different runway environments. The results validate the robustness and reconfiguration control capability of the proposed method, which improves AABS safety as well as braking efficiency
Application of Deep Reinforcement Learning in Reconfiguration Control of Aircraft Anti-Skid Braking System
The aircraft anti-skid braking system (AABS) plays an important role in aircraft taking off, taxiing, and safe landing. In addition to the disturbances from the complex runway environment, potential component faults, such as actuators faults, can also reduce the safety and reliability of AABS. To meet the increasing performance requirements of AABS under fault and disturbance conditions, a novel reconfiguration controller based on linear active disturbance rejection control combined with deep reinforcement learning was proposed in this paper. The proposed controller treated component faults, external perturbations, and measurement noise as the total disturbances. The twin delayed deep deterministic policy gradient algorithm (TD3) was introduced to realize the parameter self-adjustments of both the extended state observer and the state error feedback law. The action space, state space, reward function, and network structure for the algorithm training were properly designed, so that the total disturbances could be estimated and compensated for more accurately. The simulation results validated the environmental adaptability and robustness of the proposed reconfiguration controller
Application of Deep Reinforcement Learning in Reconfiguration Control of Aircraft Anti-Skid Braking System
The aircraft anti-skid braking system (AABS) plays an important role in aircraft taking off, taxiing, and safe landing. In addition to the disturbances from the complex runway environment, potential component faults, such as actuators faults, can also reduce the safety and reliability of AABS. To meet the increasing performance requirements of AABS under fault and disturbance conditions, a novel reconfiguration controller based on linear active disturbance rejection control combined with deep reinforcement learning was proposed in this paper. The proposed controller treated component faults, external perturbations, and measurement noise as the total disturbances. The twin delayed deep deterministic policy gradient algorithm (TD3) was introduced to realize the parameter self-adjustments of both the extended state observer and the state error feedback law. The action space, state space, reward function, and network structure for the algorithm training were properly designed, so that the total disturbances could be estimated and compensated for more accurately. The simulation results validated the environmental adaptability and robustness of the proposed reconfiguration controller
Identification of selection signals by large-scale whole-genome resequencing of cashmere goats
Abstract Inner Mongolia and Liaoning cashmere goats are two outstanding Chinese multipurpose breeds that adapt well to the semi-arid temperate grassland. These two breeds are characterized by their soft cashmere fibers, thus making them great models to identify genomic regions that are associated with cashmere fiber traits. Whole-genome sequencing of 70 cashmere goats produced more than 5.52 million single-nucleotide polymorphisms and 710,600 short insertions and deletions. Further analysis of these genetic variants showed some population-specific molecular markers for the two cashmere goat breeds that are otherwise phenotypically similar. By analyzing F ST and θπ outlier values, we identified 135 genomic regions that were associated with cashmere fiber traits within the cashmere goat populations. These selected genomic regions contained genes, which are potential involved in the production of cashmere fiber, such as FGF5, SGK3, IGFBP7, OXTR, and ROCK1. Gene ontology enrichment analysis of identified short insertions and deletions also showed enrichment in keratinocyte differentiation and epidermal cell differentiation. These findings demonstrate that this genomic resource will facilitate the breeding of cashmere goat and other Capra species in future