Distance Distribution Research Articles

Chromatin structure from high resolution microscopy: Scaling laws and microphase separation.

Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50nm) of the three-dimensional physical location of multiple (up to ∼10^{2}) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr21 obtained from multiplexed fluorescence in situ hybridization (FISH) methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags with the aim being to unravel the chromatin conformational arrangements. We show that for any specific genomic site, there are (at least) two different conformational arrangements of chromatin, implying coexisting distinct topologies which we refer to as phase α and phase β. These two phases show different scaling behaviors: the former is consistent with a crumpled globule, while the latter indicates a confined, but more extended conformation, such as a looped domain. The identification of these distinct phases sheds light on the coexistence of multiple chromatin topologies and provides insights into the effects of cellular context and/or treatments on chromatin structure.

Fractal Spatial Distributions of Initial Shear Stress and Frictional Properties on Faults and Their Impact on Dynamic Earthquake Rupture

ABSTRACT We investigate the influence of the heterogeneous slip-weakening distance (DC) in dynamic rupture simulations, in which DC is proportional to the fault irregularities. Specifically, we compare a heterogeneous fractal DC distribution to a uniform DC over the entire fault when the initial shear stress is also heterogeneous. We find that even small changes in the average value of DC (<1 mm) can lead to significant differences in the rupture evolution; that is, the average DC and the way DC is distributed determines if the rupture is a runaway, self-arrested, or nonpropagating. We find that the self-arrested ruptures differ from runaway ruptures in the amount of area characterized by large slips (asperities). Self-arrested ruptures match the Somerville et al. (1999) asperity criteria in which ∼25% of ruptured area radiate ∼45% of the total seismic moment. This criterion is not satisfied for runaway ruptures. For runaway ruptures, ∼50% of the ruptured area radiates about 70% of the seismic moment, indicating that the ruptured area is not linearly proportional to the seismic moment. Self-arrested ruptures are characterized by dynamic shear stress drops (SDs) in the range ∼2.9–5.5 MPa, whereas for runaway ruptures the dynamic SDs increase to values between ∼12 and 20 MPa. Self-arrested ruptures generated by fractal distributed DC resemble the rupture properties of observed earthquakes. In addition, results show that the conditions for self-arrested ruptures are connected to the decrease of residual energy at rupture boundaries.

Exploring the dynamics and structure of PpiB in living Escherichiacoli cells using electron paramagnetic resonance spectroscopy.

The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.

Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid.

The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.

Bioorthogonal Labeling Enables In Situ Fluorescence Imaging of Expressed Gas Vesicle Nanostructures.

Gas vesicles (GVs) are proteinaceous nanostructures that, along with virus-like particles, encapsulins, nanocages, and other macromolecular assemblies, are being developed for potential biomedical applications. To facilitate such development, it would be valuable to characterize these nanostructures' subcellular assembly and localization. However, traditional fluorescent protein fusions are not tolerated by GVs' primary constituent protein, making optical microscopy a challenge. Here, we introduce a method for fluorescently visualizing intracellular GVs using the bioorthogonal label FlAsH, which becomes fluorescent upon reaction with the six-amino acid tetracysteine (TC) tag. We engineered the GV subunit protein, GvpA, to display the TC tag and showed that GVs bearing TC-tagged GvpA can be successfully assembled and fluorescently visualized in HEK 293T cells. Importantly, this was achieved by replacing only a fraction of GvpA with the tagged version. We used fluorescence images of the tagged GVs to study the GV size and distance distributions within these cells. This bioorthogonal and fractional labeling approach will enable research to provide a greater understanding of GVs and could be adapted to similar proteinaceous nanostructures.

The study of angular distance distribution to the solar flares during different solar cycles

The angular distance of the solar flares to the projective point of the center of the solar disk on the solar spherical surface has been studied by the heliographical or helioprojective coordinates, during the periods 1975–2021 for GOES events and 2002–2021 for RHESSI events, hereafter “distance.” It gives a specific distribution curvature. It has also been noted that when using the number of solar flare events in each satellite, GOES or RHESSI, or even using the sum of the flux (class) or importance parameter, it obtains the same result, which is that the shape of the distribution curve remains in its shape without any significant change. In addition, it has been shown that the distribution curve contains a specific number of peaks. These peaks have a specific distance from the center of the solar disk that is very similar to the projection of the solar interior layers on the solar disk. For this reason, the names of these four main peaks have been given as follows: (1) the core circle (0–15°): it is a projection of the solar core onto the solar disk, (2) radiative ring (15–45°), and (3) the convection ring (45–55°). The limb ring is 80–90°. This result makes us wonder why the number of events in the middle of the solar disk is few, and also small at the solar limb, while many in the other parts in the solar disk. This suggests that we need to understand the sun better than before, and it also suggests that solar flares are connected to each other through the solar interior layers, the extent of which may reach the convection zone or perhaps beyond that, or the opacity of the convection zone may be less than the currently estimated value.

Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET

Proteins are the workhorses of biology, orchestrating a myriad of cellular functions through intricate conformational changes. Protein allostery, the phenomenon where binding of ligands or environmental changes induce conformational rearrangements in the protein, is fundamental to these processes. We have previously shown that transition metal Förster resonance energy transfer (tmFRET) can be used to interrogate the conformational rearrangements associated with protein allostery and have recently introduced novel FRET acceptors utilizing metal-bipyridyl derivatives to measure long (>20 Å) intramolecular distances in proteins. Here, we combine our tmFRET system with fluorescence lifetime measurements to measure the distances, conformational heterogeneity, and energetics of maltose-binding protein, a model allosteric protein. Time-resolved tmFRET captures near-instantaneous snapshots of distance distributions, offering insights into protein dynamics. We show that time-resolved tmFRET can accurately determine distance distributions and conformational heterogeneity of proteins. Our results demonstrate the sensitivity of time-resolved tmFRET in detecting subtle conformational or energetic changes in protein conformations, which are crucial for understanding allostery. In addition, we extend the use of metal-bipyridyl compounds, showing that Cu(phen)2+ can serve as a spin label for pulse dipolar electron paramagnetic resonance (EPR) spectroscopy, a method that also reveals distance distributions and conformational heterogeneity. The EPR studies both establish Cu(phen)2+ as a useful spin label for pulse dipolar EPR and validate our time-resolved tmFRET measurements. Our approach offers a versatile tool for deciphering conformational landscapes and understanding the regulatory mechanisms governing biological processes.

Extended Lorenz majorization and frequencies of distances in an undirected network

Abstract Purpose To contribute to the study of networks and graphs. Design/methodology/approach We apply standard mathematical thinking. Findings We show that the distance distribution in an undirected network Lorenz majorizes the one of a chain. As a consequence, the average and median distances in any such network are smaller than or equal to those of a chain. Research limitations We restricted our investigations to undirected, unweighted networks. Practical implications We are convinced that these results are useful in the study of small worlds and the so-called six degrees of separation property. Originality/value To the best of our knowledge our research contains new network results, especially those related to frequencies of distances.

Real-World Molecular Out-Of-Distribution: Specification and Investigation.

This study presents a rigorous framework for investigating molecular out-of-distribution (MOOD) generalization in drug discovery. The concept of MOOD is first clarified through a problem specification that demonstrates how the covariate shifts encountered during real-world deployment can be characterized by the distribution of sample distances to the training set. We find that these shifts can cause performance to drop by up to 60% and uncertainty calibration by up to 40%. This leads us to propose a splitting protocol that aims to close the gap between the deployment and testing. Then, using this protocol, a thorough investigation is conducted to assess the impact of model design, model selection, and data set characteristics on MOOD performance and uncertainty calibration. We find that appropriate representations and algorithms with built-in uncertainty estimation are crucial to improving performance and uncertainty calibration. This study sets itself apart by its exhaustiveness and opens an exciting avenue to benchmark meaningful algorithmic progress in molecular scoring.

Goodbye to Chi by Eye: A Bayesian Analysis of Photometric Binaries in Six Open Clusters

We present a robust methodology for identifying photometric binaries in star clusters. Using Gaia DR3, Pan-STARRS, and Two Micron All Sky Survey data, we self-consistently define the cluster parameters and binary demographics for the open clusters (OCs) NGC 2168 (M35), NGC 7789, NGC 6819, NGC 2682 (M67), NGC 188, and NGC 6791. These clusters span in age from ∼200 Myr (NGC 2168) to more than ∼8 Gyr (NGC 6791) and have all been extensively studied in the literature. We use the Bayesian Analysis of Stellar Evolution software suite to derive the age, distance, reddening, metallicity, binary fraction, and binary mass-ratio posterior distributions for each cluster. We perform a careful analysis of our completeness and also compare our results to previous spectroscopic surveys. For our sample of main-sequence stars with masses between 0.6 and 1 M ⊙, we find that these OCs have similar binary fractions that are also broadly consistent with the field multiplicity fraction. Within the clusters, the binary fraction increases dramatically toward the cluster centers, likely a result of mass segregation. Furthermore nearly all clusters show evidence of mass segregation within the single and binary populations. The OC binary fraction increases significantly with cluster age in our sample, possibly due to a combination of mass-segregation and cluster-dissolution processes. We also find a hint of an anticorrelation between binary fraction and cluster central density as well as total cluster mass, possibly due to an increasing frequency of higher-energy close stellar encounters that inhibit long-period binary survival and/or formation.

Impact assessment of the Australian 2019–20 megafires on roost sites of the vulnerable grey-headed flying-fox (Pteropus poliocephalus)

Bushfires are a natural component of the ecology of many landscapes, but megafires such as those experienced in Australia between July 2019 and April 2020 have substantial direct and indirect impacts on wildlife. Following these megafires, bushfires have begun to be considered a significant emerging threat to the vulnerable grey-headed flying-fox (Pteropus poliocephalus). In this study, we quantified the impact of the 2019–20 megafires on all known roost locations of the species by (1) determining the number of roosts within burnt areas represented by three fire severity mapping products, (2) classifying burnt roosts according to the severity with which they burnt, and (3) examining the distribution of distances to the nearest burnt areas for unburnt roosts. Our findings indicate that the impacts of the 2019–20 megafires on roosting habitat of the grey-headed flying-fox have hitherto been underestimated. Of 874 known grey-headed flying-fox roosts, we found that 134 roosts were situated within burnt areas, equating to 15 % of the species’ roost locations. Depending on the mapping products applied, part or all canopy vegetation was severely burnt in 27–36 % of burnt roosts, while in 11–14 % of burnt roosts, the canopy vegetation was burnt entirely. Of the 740 unburnt roosts, 50 % were located within 6.85 km from burnt areas, suggesting that, at a substantial number of roosts, flying-foxes were also indirectly affected by the fires, through the effects of smoke on roosting and locally foraging individuals, and through destruction of local foraging resources from burning. We discuss the implications of these findings for the conservation management of this vulnerable species.

Ensemble structure of the N-terminal domain (1–267) of FUS in a biomolecular condensate

Solutions of some proteins phase separate into a condensed state of high protein concentration and a dispersed state of low concentration. Such behavior is observed in living cells for a number of RNA-binding proteins that feature intrinsically disordered domains. It is relevant for cell function via the formation of membraneless organelles and transcriptional condensates. On a basic level, the process can be studied in vitro on protein domains that are necessary and sufficient for liquid-liquid phase separation (LLPS). We have performed distance distribution measurements by electron paramagnetic resonance for 13 sections in an N-terminal domain (NTD) construct of the protein fused in sarcoma (FUS), consisting of the QGSY-rich domain and the RGG1 domain, in the denatured, dispersed, and condensed state. Using 10 distance distribution restraints for ensemble modeling and three such restraints for model validation, we have found that FUS NTD behaves as a random-coil polymer under good-solvent conditions in both the dispersed and condensed state. Conformation distribution in the biomolecular condensate is virtually indistinguishable from the one in an unrestrained ensemble, with the latter one being based on only residue-specific Ramachandran angle distributions. Over its whole length, FUS NTD is slightly more compact in the condensed than in the dispersed state, which is in line with the theory for random coils in good solvent proposed by de Gennes, Daoud, and Jannink. The estimated concentration in the condensate exceeds the overlap concentration resulting from this theory. The QGSY-rich domain is slightly more extended, slightly more hydrated, and has slightly higher propensity for LLPS than the RGG1 domain. Our results support previous suggestions that LLPS of FUS is driven by multiple transient nonspecific hydrogen bonding and π−sp2 interactions.

Numerical study on perforation damage and fragmentation of reinforced concrete slab under close-in explosion

Reinforced concrete (RC) structure is prone to suffer localized damage when exposed to close-in explosions. Spalling damage might occur due to the reflected tensile stress wave exceeding the concrete dynamic tensile strength. When the blast wave is intensive enough, it can also cause significant crushing damage on the contact surface, potentially leading to perforation when the crushing depth aligns with the spalling depth. This perforation/spalling damage can generate a large number of secondary fragments with high ejecting velocities. Additionally, the blast wave might pass through the perforation hole and cause further acceleration of the secondary fragments. In the author’s previous study, an ALE-FEM-SPH numerical model was established and validated with the existing testing data for the prediction of spalling damage as well as fragment sizes and velocities. As a continuous work, this study conducts numerical simulations to predict the perforation damage and fragmentation under higher-intensity blast loading. The results including centre perforation hole, spalling area on back surface, fragment ejecting velocities, fragment landing distance and fragment characteristics distributions are reported and studied. The acceleration effect on the secondary fragments by the traversed blast wave that further carries the fragments flying is also investigated. The numerical results show that using the scaled distance Z might not reliably quantify the perforation/spalling damage under close-in cylindrical TNT explosion. Given the identical scaled distance, the scenarios with different combinations of charge weight and standoff distance can result in large variations up to 300% in the predictions of damaged area and 50% for the maximum fragment ejecting velocities, respectively. A scaled blast parameter Z* is suggested and the empirical formulae are proposed for better quantification of the damaged area of RC slab as well as the fragment velocity and kinetic energy under close-in cylindrical TNT explosions.

Ice‐Bridging Frustration by Self‐Ejection of Single Droplets Results in Superior Anti‐Frosting Surfaces

AbstractSurfaces capable of delaying the frosting passively and facilitating its removal are highly desirable in fields where ice introduces inefficiencies and risks. Coalescence‐induced condensation droplets jumping (CICDJ), enabled on highly hydrophobic surfaces, is already exploited to slow down the frosting but it is insufficient to completely eliminate the propagation by ice‐bridging. The study shows here how the self‐ejection of single condensation droplets can fully frustrate all the ice bridges, resulting in a frost velocity lower than 0.5 µm s−1 and thus falling below the current limits of passive surfaces. Arrays of truncated microcones, covered by uniformly hydrophobic nanostructures, enable individual condensation droplets to grow and self‐propel toward the top of the microstructures and then to self‐eject once a precise volume is reached. The independency of self‐ejection on the neighbor droplets allows a fine control of the droplets size and distance distributions and thus the ice‐bridging frustration. The truncated microcones with the smallest heads area fraction maximize the percentage of self‐ejecting droplets and minimize the frost velocity. The ice bridges frustration also implies a small frost area coverage, highly desirable in aeronautics and thermal machines.

Methodology to Investigate Effect of Prosthetic Interface Design on Residual Limb Soft Tissue Deformation.

Residual limb discomfort and injury is a common experience for people living with lower limb amputation. Frequently, inadequate load distribution between the prosthetic device and the residual limb is the root cause of this issue. To advance our understanding of prosthetic interface fit, tools are needed to evaluate the mechanical interaction at the prosthetic interface, allowing interface designs to be evaluated and optimised. Present a methodology report designed to facilitate comprehension of the mechanical interaction between the prosthetic interface and the residual limb. As a pilot study, this methodology is used to compare a hands-on and hands-off interface for a single transtibial prosthesis user using secondary Magnetic Resonance Imaging (MRI) data. MRI data of the residual limb while wearing a prosthetic interface is segmented into a hard tissue and a skin surface model. These models are exported as stereolithography (STL) files. Two methods are used to analyse the interface designs. Firstly, CloudCompare software is used to compute the nearest vertex on the skin surface for every vertex on the compiled internal bony surface for both interface types. Secondly, CloudCompare software is used to compare registered skin surfaces of the residual limb while wearing the hands-on and hands-off interfaces. The maximum and minimum nearest distances between the internal bony surface and skin surface were similar between interface types. However, the distribution of nearest distances was different. When comparing the skin surface while wearing both interfaces, where the fit is more compressive can be visualized. For the dataset used in this study, the classic features of a hands-on Patella Tendon Bearing interface and hands-off pressure cast interface could be identified. The methodology presented in this report may give researchers a further tool to better understand how interface designs affect the soft tissues of the residual limb.

Conformational Distribution of a Multidomain Protein Measured by Single-Pair Small-Angle X-ray Scattering.

The difficulty in evaluating the conformational distribution of proteins in solution often hinders mechanistic insights. One possible strategy for visualizing conformational distribution is distance distribution measurement by single-pair small-angle X-ray scattering (SAXS), in which the scattering interference from only a specific pair of atoms in the target molecule is extracted. Despite this promising concept, with few applications in synthetic small molecules and DNA, technical difficulties have prevented its application in protein conformational studies. This study used a synthetic tag to fix the lanthanide ion at desired sites on the protein and used single-pair SAXS with contrast matching to evaluate the conformational distribution of the multidomain protein enzyme MurD. These data highlighted the broad conformational and ligand-driven distribution shifts of MurD in solution. This study proposes an important strategy in solution structural biology that targets dynamic proteins, including multidomain and intrinsically disordered proteins.

Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations.

Protein thermodynamics is intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equilibria evolved for the physiology of the organism. Despite the importance of these equilibria for understanding biological function and developing treatments for disease, computational and experimental methods capable of quantifying the energetic determinants of these equilibria are limited to systems of modest size. Recently, it has been demonstrated that the artificial intelligence system AlphaFold2 can be manipulated to produce structurally valid protein conformational ensembles. Here, we extend these studies and explore the extent to which AlphaFold2 contact distance distributions can approximate projections of the conformational Boltzmann distributions. For this purpose, we examine the joint probability distributions of inter-residue contact distances along functionally relevant collective variables of several protein systems. Our studies suggest that AlphaFold2 normalized contact distance distributions can correlate with conformation probabilities obtained with other methods but that they suffer from peak broadening. We also find that the AlphaFold2 contact distance distributions can be sensitive to point mutations. Overall, we anticipate that our findings will be valuable as the community seeks to model the thermodynamics of conformational changes in large biomolecular systems.

Transform-Equivariant Consistency Learning for Temporal Sentence Grounding

This paper addresses the temporal sentence grounding (TSG). Although existing methods have made decent achievements in this task, they not only severely rely on abundant video-query paired data for training, but also easily fail into the dataset distribution bias. To alleviate these limitations, we introduce a novel Equivariant Consistency Regulation Learning (ECRL) framework to learn more discriminative query-related frame-wise representations for each video, in a self-supervised manner. Our motivation comes from that the temporal boundary of the query-guided activity should be consistently predicted under various video-level transformations. Concretely, we first design a series of spatio-temporal augmentations on both foreground and background video segments to generate a set of synthetic video samples. In particular, we devise a self-refine module to enhance the completeness and smoothness of the augmented video. Then, we present a novel self-supervised consistency loss (SSCL) applied on the original and augmented videos to capture their invariant query-related semantic by minimizing the KL-divergence between the sequence similarity of two videos and a prior Gaussian distribution of timestamp distance. At last, a shared grounding head is introduced to predict the transform-equivariant query-guided segment boundaries for both the original and augmented videos. Extensive experiments on three challenging datasets (ActivityNet, TACoS, and Charades-STA) demonstrate both effectiveness and efficiency of our proposed ECRL framework.

An Anisotropic Side Contact Model Based on the Peak Description Method of Surface Profile

Abstract In contact models, traditional profile description methods are based on all sampling points of the profile. The methods can only describe the features in the height direction of profile, but are difficult to describe the profile features perpendicular to the height direction, which is the main obstacle to side contact modeling. In this paper, a profile description method based on peaks is proposed, which enables the profile features perpendicular to the height direction of the profile to be expressed. The statistical distribution law of the horizontal distances perpendicular to the height direction of the profile between adjacent asperities on anisotropic contact surfaces is investigated for the first time, and it is found that the distribution of the horizontal distances is very close to the normal distribution, but the values are different in different texture directions. The distribution law of the height differences between adjacent asperities is also investigated and is found to be close to a normal distribution, but the numerical values are different from the normal distribution of profile heights. Based on the results, the distribution function of the contact angle widely used in side contact model is replaced, and a new side contact model is proposed. By the model, the effects of the statistical parameters of surface profile and the material parameters of surfaces on the surface contact characteristics are investigated. The results of investigation show that the effect of the standard deviations of the horizontal distances between asperities in different texture directions on the normal contact stiffness between surfaces is obvious, and the normal contact stiffness will decrease with the increase of the standard deviation of the horizontal distances in any direction.

Phylogenetically evolutionary analysis provides insights into the genetic diversity and adaptive evolution of porcine deltacoronavirus

BackgroundPorcine deltacoronavirus (PDCoV) is one of the emerging swine enteric coronaviruses (SECoVs), which has been widely prevalent in the North America and Asia. In addition to causing severe diarrhea in piglets, PDCoV also shows the potential to infect diverse host species, including calves, chickens, turkey poults, and humans. However, the clinical pathogenicity and genetic evolution of PDCoV is still not fully understood.ResultsHere, we recorded an outbreak of a novel recombinant PDCoV strain (CHN-HeN06-2022) in a large nursery fattening pig farm. Genomic analysis showed that the CHN-HeN06-2022 strain shared 98.3-98.7% sequence identities with the Chinese and American reference strains. To clarify the evolutionary relationships, phylogenetic analysis was performed using the PDCoV genome sequences available in the GenBank database. Based on genetic distance and geographical distribution, the phylogenetic tree clearly showed that all the PDCoV sequences could be divided into lineage 1 and lineage 2, which were further classified into sublineage 1.1 (Chinese strains), 1.2 (the North American strains), 2.1 (the Southeast Asian strains), and 2.2 (Chinese strains). Corresponding to the evolutionary tree, we found that, compared to lineage 1, lineage 2 strains usually contain a continuous 6-nt deletion in Nsp2 and a 9-nt deletion in Nsp3, respectively. Furthermore, recombination analysis suggested that the CHN-HeN06-2022 occurred segments exchange crossed Nsp2 and Nsp3 region between sublineage 1.1 and sublineage 2.1. Combined with previously reported recombinant strains, the highest recombination frequency occurred in Nsp2, Nsp3, and S gene. Additionally, we identified a total of 14 amino acid sites under positive selection in spike protein, most of which are located in the regions related with the viral attachment, receptor binding, and membrane fusion.ConclusionsTaken together, our studies provide novel insights into the genetic diversity and adaptive evolution of PDCoV. It would be helpful to the development of vaccine and potential antiviral agent.