Biology subjects

Chen, N.

Publications and source records attributed to Chen, N..

At least 127 records · Page 7Linked to original sources

bioRxiv2021

Serine 182 on RORγt regulates T helper 17 and regulatory T cell functions to resolve inflammation

Intestine homeostasis is maintained by the delicate balance of Th17 effector cells and Treg cells. Dysregulation of these cell populations contributes to inflammation, tissue damage, and chronic conditions. ROR{gamma}t is essential for the differentiation of Th17 and a subset of Treg (ROR{gamma}t+ Treg) cells involved in intestinal inflammation. ROR{gamma}t belongs to the nuclear receptor family of transcription factors with hinge regions that are highly flexible for co-activator/co-repressor interactions. Serine 182 at the hinge region of ROR{gamma}t is phosphorylated. This study aims to uncover how S182 on ROR{gamma}t contributes to mucosal homeostasis and diseases. We used CRISRP technology to generate a phosphor-null knock-in mutant mouse line (ROR{gamma}tS182A) to assess its role in intestine physiology. scRNA-seq was performed on WT and ROR{gamma}tS182A cohoused littermates to evaluate colonic T cell heterogeneity under steady state and colitis settings. Single-cell transcriptomics revealed that ROR{gamma}tS182 maintains colonic T cell heterogeneity under steady state, without interfering T cell development and differentiation. In inflamed tissues, ROR{gamma}tS182 simultaneously restricts IL-1{beta}-mediated Th17 activities and promotes anti-inflammatory cytokine IL-10 production in LT-like Treg cells. Phospho-null ROR{gamma}tS182A knock-in mice challenged with DSS induced colitis and EAE experienced delayed recovery and exacerbated pathology. The double switch role of ROR{gamma}tS182 is critical in resolving T cell-mediated inflammation and provides a potential therapeutic target to combat autoimmune diseases.

immunology↗

bioRxiv2021

Modulation of fatty acid elongation generates sexually dimorphic hydrocarbons and female attractiveness in Blattella germanica (L.)

Insect cuticular hydrocarbons (CHCs) serve as important intersexual signaling chemicals and generally show variation between the sexes, but little is known about the generation of sexually dimorphic hydrocarbons (SDHCs) in insects. Here, we report the molecular mechanism and biological significance that underling the generation of SDHC in the German cockroach, Blattella germanica. Sexually mature females possess more C29 cuticular hydrocarbons (CHCs), especially the contact sex pheromone precursor 3,11-DimeC29. RNAi screen against fatty acid elongase gene family members and combined with heterologous expression revealed that both BgElo12 and BgElo24 were involved in HC production, but BgElo24 is of wide catalytic activities and is able to provides substrates for BgElo12, and only the female-enriched BgElo12 was responsible for sustaining female-specific HC profile. Repressing BgElo12 masculinized the female CHC profile, decreased contact sex pheromone level and consequently reduced the sexual attractiveness of female cockroaches. Moreover, the asymmetric expression of BgElo12 between the sexes is modulated by sex differentiation cascade. Specifically, male-specific BgDsx represses the transcription of BgElo12 in males, while BgTra is able to remove this effect in females. Our study reveals a novel molecular mechanism responsible for the formation of SDHCs, and also provide evidences on shaping of the SDHCs by sexual selection, as females use them to generate high levels of contact sex pheromone.

molecular biology↗

bioRxiv2020

Targeting Allostery in the Dynein Motor Domain with Small Molecule Inhibitors

Cytoplasmic dyneins are AAA (ATPase associated with diverse cellular activities) motor proteins responsible for microtubule minus-end-directed intracellular transport. Dyneins unusually large size, four distinct nucleotide-binding sites, and the existence of closely-related isoforms with different functions, pose challenges for the design of potent and selective chemical inhibitors. Here we use structural approaches to develop a model for the inhibition of a well-characterized S. cerevisiae dynein construct by pyrazolo-pyrimidinone-based compounds. These data, along with single molecule experiments and mutagenesis studies, indicate that the compounds likely inhibit dynein by engaging the regulatory ATPase sites in the AAA3 and AAA4 domains, and not by interacting with dyneins main catalytic site in the AAA1 domain. A double Walker B mutant in AAA3 and AAA4 is an inactive enzyme, suggesting that inhibiting these regulatory sites can have a similar effect to inhibiting AAA1. Our findings reveal how chemical inhibitors can be designed to disrupt allosteric communication across dyneins AAA domains.

biochemistry↗

bioRxiv2020

Neuronal circuitry underlying female aggression in Drosophila

Aggressive social interactions are used to compete for limited resources and are regulated by complex sensory cues and the organisms internal state. While both sexes exhibit aggression, its neuronal underpinnings are understudied in females. Here, we describe a set of connected neurons in the adult Drosophila melanogaster central brain that drive female aggression. We identified a population of sexually dimorphic aIPg neurons whose optogenetic activation increased, and genetic inactivation reduced, female aggression. Analysis of GAL4 lines identified in an unbiased screen for increased female chasing behavior revealed the involvement of another sexually dimorphic neuron, pC1d, and implicated pC1d and aIPg neurons as core nodes regulating female aggression. pC1d activation increased female aggression and electron microscopy (EM) connectomic analysis demonstrated that aIPg neurons and pC1d have strong reciprocal connections. Our work reveals important regulatory components of the neuronal circuitry that underlies female aggressive social interactions and provides tools for their manipulation.

neuroscience↗

bioRxiv2020

WOX9 functions antagonistic to STF and LAM1 to regulate leaf blade expansion in Medicago truncatula and Nicotiana sylvestris

Plant specific WOX family transcription factors are known to regulate embryogenesis, meristem maintenance and lateral organ development. Modern clade WOX genes function through a transcriptional repression mechanism, and the intermediate clade transcriptional activator WOX9 functions with the repressor WOX genes in embryogenesis and meristems maintenance, but the mechanism of this interaction is unclear. WOX1 homologues STF and LAM1 are required for leaf blade outgrowth in Medicago truncatula and Nicotiana Sylvestris, respectively. Here we show that WOX9 negatively regulates leaf blade outgrowth and functions antagonistically to STF and LAM1. While NsWOX9 ectopic expression enhances the lam1 mutant phenotype, and antisense expression partially rescues the lam1 mutant, both overexpression of NsWOX9 and knockout by CRISPR/Cas9 genome editing in N. sylvestris resulted in a range of severe leaf blade distortions, indicating that controlled negative regulation by NsWOX9 is required for proper blade development. Our results indicate that direct repression of WOX9 transcriptional activation activity by the transcriptional repressor STF/LAM1 is required for correct blade architecture and patterning in M. truncatula and N. sylvestris. These findings suggest that a balance between transcriptional activation and repression mechanisms by direct interaction of activator and repressor WOX genes may be required for cell proliferation and differentiation homeostasis, and could be an evolutionarily conserved mechanism for the development of complex and diverse morphology in higher plants. One sentence summaryWOX9 negatively regulates blade outgrowth antagonizing STF function but directly repressed by STF indicating WOX-mediated homeostasis in cell proliferation and differentiation during leaf morphogenesis.

plant biology↗

bioRxiv2020

redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-Cell RNA-Seq Data and Applications in Cancer

Recent advancement of single-cell RNA-seq technology facilitates the study of cell lineages in developmental processes as well as cancer. In this manuscript, we developed a computational method, called redPATH, to reconstruct the pseudo developmental time of cell lineages using a consensus asymmetric Hamiltonian path algorithm. Besides, we implemented a novel approach to visualize the trajectory development of cells and visualization methods to provide biological insights. We validated the performance of redPATH by segmenting different stages of cell development on multiple neural stem cell and cancerous datasets, as well as other single-cell transcriptome data. In particular, we identified a subpopulation of malignant glioma cells, which are stem cell-like. These cells express known proliferative markers such as GFAP (also identified ATP1A2, IGFBPL1, ALDOC) and remain silenced in quiescent markers such as ID3. Furthermore, MCL1 is identified as a significant gene that regulates cell apoptosis, and CSF1R confirms previous studies for re-programming macrophages to control tumor growth. In conclusion, redPATH is a comprehensive tool for analyzing single-cell RNA-Seq datasets along a pseudo developmental time. The software is available via http://github.com/tinglab/redPATH.

bioinformatics↗

bioRxiv2020

Inferring Multiple Metagenomic Association Networks based on Variation of Environmental Factors

Identifying significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose, but they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors, which can result in inaccurate estimations. We propose a computational model, k-Lognormal-Dirichlet-Multinomial model (kLDM), which estimates multiple association networks that correspond to specific environmental conditions according to values of environmental factors (EFs), and simultaneously infers microbe-microbe and environmental factor-microbe associations for each network. We showed the effectiveness of kLDM on synthetic data, a colorectal cancer dataset, as well as the TARA Oceans and American Gut project datasets. The results showed that the widely used Spearmans rank correlation coefficient (SCC) performed much worse than other methods, indicating the importance of separating samples by environmental conditions. We compared cancer fecal samples with cancer-free samples, and our estimation showed fewer associations among microbes but stronger associations between specific bacteria such as five colorectal cancer (CRC)-associated OTUs, indicating gut microbe translocation in cancer patients. Some environmental-factor-dependent associations were found within marine eukaryotic community, and gut microbial heterogeneity of irritable bowel disease (IBD) patients was detected. Results demonstrated that kLDM could successfully unravel the underlying biological associations. In summary, our study presents a computational framework that can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and python scripts, together with all experimental datasets are all accessible at Github (https://github.com/tinglab/kLDM.git).

bioinformatics↗

bioRxiv2020

Sequence-based Prediction of Metamorphic Behavior in Proteins

An increasing number of proteins have been demonstrated in recent years to adopt multiple three-dimensional folds with different functions. These metamorphic proteins are characterized by having two or more folds with significant differences in their secondary structure, where each fold is stabilized by a distinct local environment. So far, about 90 metamorphic proteins have been identified in the Protein Databank (PDB), but we and others hypothesize that a far greater number of metamorphic proteins remain undiscovered. In this work, we introduce a computational model to predict metamorphic behavior in proteins using only knowledge of the sequence. In this model, secondary structure prediction programs are used to calculate diversity indices, which are measures of uncertainty in predicted secondary structure at each position in the sequence; these are then used to assign protein sequences as likely to be metamorphic vs. monomorphic (i.e. having just one-fold). We constructed a reference dataset to train our classification method, which includes a novel compilation of 140 likely-monomorphic proteins, and a set of 201 metamorphic proteins taken from the literature. Our model is able to classify proteins as metamorphic vs. monomorphic with a Matthews correlation coefficient of [~]0.4 and true positive / true negative rates of [~]65% / 80%, suggesting that it is possible to predict metamorphic behavior in proteins using only sequence information. Statement of SignificanceThis paper introduces the diversity index as a descriptor to distinguish metamorphic proteins, which possess multiple stable folds, from monomorphic proteins that possess only one fold. The diversity index is designed to measure uncertainty in computationally predicted secondary structure, which we hypothesize is elevated for metamorphic proteins. We tested our hypothesis by training a binary classifier using the diversity index and an annotated dataset of metamorphic and monomorphic proteins, and found an optimal Matthews correlation coefficient of 0.4, supporting the hypothesis and demonstrating for the first time that it is possible to predict metamorphic behavior in proteins using only sequence information. The sequence-based classifier has broader applicability compared to methods that rely on making comparison to experimentally measured structures.

biophysics↗

bioRxiv2020

Microbial redox activity mediated anaerobic pyrite oxidation under circumneutral conditions

In modern Earth, anaerobic pyrite oxidation under circumneutral conditions also has great impact on the fate of nitrate in aquifers and sediments, as well as the transportation of toxic metals. However, the mechanism of how microbes mediated this process is still being debated. Electrochemical analysis on pyrite cubic electrode showed that, its oxidation threshold under anaerobic circumneutral conditions (ca. 200 mV) was much lower than that at aerobic acidic conditions (ca. 650 mV), implying possible direct pyrite oxidation by high redox potential cellular components. Sole substrate (pyrite) microbial enrichment cultures with EDTA addition showed higher oxidation rate (0.092 d-1) than that of EDTA-free cultures (0.019 d-1), suggesting that ligands producing pathway was much preferred by microbes than maintaining acidic micro-environments. This hypothesis was supported by amplicon and metagenomic sequencing data, which demonstrated discrepant bacteria involving iron-sulfur oxidation and metabolic potentials in cultures with/without EDTA addition. A concept model was proposed based on experimental data considering different reaction stages and microbial communities. The results shed lights on the potential interactions between microbes and pyrite, which may serve as a model for explaining subsurface pyrite oxidation and optimizing anaerobic pyrite oxidation-based pollutant removal processes. TOC art O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/952168v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@14c7a01org.highwire.dtl.DTLVardef@1de10bdorg.highwire.dtl.DTLVardef@1ceb4dorg.highwire.dtl.DTLVardef@9c27fc_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

HSI2/VAL1 and HSL1/VAL2 function redundantly to regulate seed dormancy by controlling DOG1 expression in Arabidopsis

DELAY OF GERMINATION1 (DOG1) represents a major quantitative locus for the genetic regulation of seed dormancy in Arabidopsis. Accumulation of DOG1 in seeds leads to deep dormancy and delayed germination. Here, we report that the conserved B3 DNA binding domains of the transcriptional repressors HIGH-LEVEL EXPRESSION OF SUGAR INDICIBLE GENE2/ VIVIPAROUS-1/ABSCISIC ACID INSENSITIVE 3-LIKE1 (HSI2/VAL1) and HSI2-LIKE1/ VIVIPAROUS-1/ABSCISIC ACID INSENSITIVE 3-LIKE2 (HSL1/VAL2), which play critical roles in the developmental transition from seed maturation to seedling growth, interact with RY elements in the DOG1 proximal promoter leading to repression of DOG1 transcription during germination and seedling establishment. DOG1 expression is partially de-repressed in hsi2/val1 (hsi2-2) but not in hsl1/val2 (hsl1-1) knockout mutants and is strongly upregulated in a hsi2/val1 hsl1/val2 double mutant, indicating that HSI2/VAL1 and HSL1/VAL2 act redundantly to repress DOG1 expression. HSI2/VAL1 and HSL1/VAL2 form homo- and hetero-dimers in vivo, and dimerization is dependent on the HSI2/VAL1 PHD-like domain. Complementation of hsi2-2 with HSI2/VAL1 harboring a disrupted plant homeodomain (PHD)-like domain results in stronger de-repression of DOG1 expression than the hsi2-2 knockout, indicating that the PHD-like domain plays a critical role in mediating functional interactions between HSI2/VAL1 and HSL1/VAL2. Both HSI2/VAL1 and HSL1/VAL2 interact with components of polycomb repressive complex 2 (PRC2), including CURLY LEAF and MULTICOPY SUPPRESSOR OF IRA1 (MSI1), along with LIKE HETERCHROMATIN PROTEIN 1 (LHP1), which are involved in the deposition and expansion of histone H3 lysine 27 trimethylation (H3K27me3) marks in repressive chromatin. Thus, HSI2/VAL1 HSL1/VAL2-dependent recruitment of PRC2 leads to silencing of DOG1 through the deposition of H3K27me3.

molecular biology↗

bioRxiv2019

Effective Combination Immunotherapy using Oncolytic Viruses to Deliver CAR Targets to Solid Tumors

Chimeric antigen receptor (CAR)-engineered T cell therapy for solid tumors is limited by the lack of tumor-restricted and homogeneous expression of tumor antigens1,2. Therefore, we engineered an oncolytic virus to express a non-signaling, truncated CD19 (CD19t) protein for tumor-selective delivery, enabling targeting by CD19-specific CAR T cells. Infecting tumor cells with a chimeric oncolytic vaccinia virus coding for CD19t (OV19t) produced de novo CD19 surface-antigen expression prior to virus-mediated tumor lysis. Co-cultured CD19-CAR T cells secreted cytokines and elicited potent cytolytic activity against infected tumors. Using multiple mouse tumor models, intratumoral delivery of OV19t induced tumor expression of CD19t and improved tumor control following CD19-CAR T cell administration. CAR T cell-mediated tumor killing also promoted release of virus from dying tumor cells, which propogated tumor expression of CD19t. These data demonstrate a novel immunotherapy approach utilizing oncolytic viruses to promote de novo CAR T cell targeting of solid tumors. One Sentence SummaryWe describe a novel and effective combination immunotherapy utilizing oncolytic viruses to deliver de novo cell surface expression of CD19 antigen promoting CD19-CAR T cell anti-tumor responses against solid tumors.

cancer biology↗

bioRxiv2019

In Vivo Neuroregeneration to Treat Ischemic Stroke in Adult Non-Human Primate Brains through NeuroD1 AAV-based Gene Therapy

Stroke is a leading cause of death and disability but most of the clinical trials have failed in the past, despite our increasing understanding of the molecular and pathological mechanisms underlying stroke. While many signaling pathways have been identified in the aftermath of stroke, the majority of current approaches are focusing on neural protection rather than neuroregeneration. In this study, we report an in vivo neural regeneration approach to convert brain internal reactive astrocytes into neurons through ectopic expression of a neural transcription factor NeuroD1 in adult non-human primate (NHP) brains following ischemic stroke. We demonstrate that NeuroD1 AAV-based gene therapy can convert reactive astrocytes into neurons with high efficiency (90%), but astrocytes are never depleted in the NeuroD1-expressed areas, consistent with the proliferative capability of astrocytes. The NeuroD1-mediated in vivo astrocyte-to-neuron (AtN) conversion in monkey cortex following ischemic stroke increased local neuronal density, reduced reactive microglia, and surprisingly protected parvalbumin interneurons in the converted areas. The NeuroD1 gene therapy showed a broad time window, from 10 days to 30 days following ischemic stroke, in terms of exerting its neuroregenerative and neuroprotective effects. The cortical astrocyte-converted neurons also showed Tbr1+ cortical neuron identity, similar to our earlier findings in rodent animal models. Unexpectedly, NeuroD1 expression in converted neurons showed a significant decrease after 6 months of viral infection, suggesting a potential self-regulatory mechanism of NeuroD1 in adult mature neurons of NHPs. These results suggest that in vivo cell conversion through NeuroD1-based gene therapy may be an effective approach to regenerate new neurons in adult primate brains for tissue repair.

neuroscience↗

bioRxiv2019

Competence to epithelialise coincides with competence to differentiate in pluripotent cells

Pluripotent cells reorganise themselves into an epithelium before they initiate differentiation, but it is not clear how these two events are mechanistically linked. Here we use quantitative imaging approaches to measure cellular rearrangements that accompany exit from naive pluripotency. We show that competence to epithelialise, like competence to differentiate, is a regulated process. The pro-differentiation transcription factor Tcf15 prospectively identifies cells that are competent to epithelialise. We identify early upregulation of the laminin receptor integrin alpha3 prior to differentiation and show that Tcf15 helps to regulate this change. Finally, we show that Tcf15 identifies and is required for efficient differentiation of a primed subpopulation of pluripotent cells. We conclude that competence to epithelialise is actively regulated and linked to differentiation-competence through the transcription factor Tcf15.

developmental biology↗

bioRxiv2019

The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures

Next-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising [~]60.44 M SNPs, [~]6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.

genomics↗

bioRxiv2019

Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment

ABSTRACT/SUMMARYOne million patients with congenital heart disease (CHD) live in the US. They have a lifelong risk of developing heart failure. Current concepts do not sufficiently address mechanisms of heart failure development specifically for these patients. We show that cardiomyocyte cytokinesis failure is increased in tetralogy of Fallot with pulmonary stenosis (ToF/PS), a common form of CHD. Labeling of a ToF/PS baby with isotope-tagged thymidine showed cytokinesis failure after birth. We used single-cell transcriptional profiling to discover that the underlying mechanism is repression of the cytokinesis gene ECT2, and show that this is downstream of {beta}-adrenergic receptors ({beta}-AR). Inactivation of the {beta}-AR genes and administration of the {beta}-blocker propranolol increased cardiomyocyte division in neonatal mice, which increased the endowment and conferred benefit after myocardial infarction in adults. Propranolol enabled the division of ToF/PS cardiomyocytes. These results suggest that {beta}-blockers should be evaluated for increasing cardiomyocyte division in patients with ToF/PS and other types of CHD.

cell biology↗

bioRxiv2019

Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project

With more than 30,000 species, fish are the largest and most ancient vertebrate group. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Here, we announce the Fish10K project, an international collaborative project or initiative? aiming to sequence 10,000 representative fish genomes under a systematic context within ten years, and officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, and sequencing and assembly strategies. To illustrate, we present the genomes of ten fish species from a cohort of 93 species chosen for technology development.

genomics↗

bioRxiv2018

Nessys: a novel method for accurate nuclear segmentation in 3D

Methods for measuring the properties of individual cells within their native 3D environment will enable a deeper understanding of embryonic development, tissue regeneration, and tumorigenesis. However current methods for segmenting nuclei in 3D tissues are not designed for situations where nuclei are densely packed, non-spherical, heterogeneous in shape, size, or texture, all of which are true of many embryonic and adult tissue types as well as in many cases for cells differentiating in culture.\n\nHere we overcome this bottleneck by devising a novel method based on labelling the nuclear envelope (NE) and automatically distinguishing individual nuclei using a tree structured ridge tracing method followed by shape ranking according to a trained classifier. The method is fast and makes it possible to process images that are larger than the computers memory. We consistently obtain accurate segmentation rates of >90% even for challenging images such as mid-gestation embryos or 3D cultures. We provide a 3D editor and inspector for the manual curation of the segmentation results as well as a program to assess the accuracy of the segmentation.\n\nWe have also generated a live reporter of the NE that can be used to track live cells in three dimensions over time. We use this to monitor the history of cell interactions and occurrences of neighbour exchange within cultures of pluripotent cells during differentiation.\n\nWe provide these tools in an open-access user-friendly format.

developmental biology↗

bioRxiv2018

Comparative whole-genome analysis reveals genetic adaptation of the invasive pinewood nematode

Genetic adaptation to new environments is essential for invasive species. To explore the genetic underpinnings of invasiveness of a dangerous invasive species, the pinewood nematode (PWN) Bursaphelenchus xylophilus, we analysed the genome-wide variations of a large cohort of 55 strains isolated from both the native and introduced regions. Comparative analysis showed abundant genetic diversity existing in the nematode, especially in the native populations. Phylogenetic relationships and principal component analysis indicate a dominant invasive population/group (DIG) existing in China and expansion beyond, with few genomic variations. Putative origin and migration paths at a global scale were traced by targeted analysis of rDNA sequences. A progressive loss of genetic diversity was observed along spread routes. We focused on variations with a low frequency allele (<50%) in the native USA population but fixation in DIG, and a total of 25,992 single nuclear polymorphisms (SNPs) were screened out. We found that a clear majority of these fixation alleles originated from standing variation. Functional annotation of these SNP-harboured genes showed that adaptation-related genes are abundant, such as genes that encode for chemoreceptors, proteases, detoxification enzymes, and proteins involved in signal transduction and in response to stresses and stimuli. Some genes under positive selection were predicted. Our results suggest that adaptability to new environments plays essentially roles in PWN invasiveness. Genetic drift, mutation and strong selection drive the nematode to rapidly evolve in adaptation to new environments, which including local pine hosts, vector beetles, commensal microflora and other new environmental factors, during invasion process.

genomics↗