Biology subjects

Shen, W.

Publications and source records attributed to Shen, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Involvement of 5' and 3' UTRs on SARS-CoV-2 Genome Packaging

The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, packages its large single-stranded RNA genome through a precise yet enigmatic mechanism. A packaging signal (PS) within its genome was proposed to facilitate the assembly of new viral particles. Here in this study, we report the role of the 5 and 3 untranslated regions (UTRs) in PS-mediated genome packaging. Utilizing proximity ligation data, we demonstrate direct interactions between the UTRs and the PS9 element, a key packaging signal within the SARS-CoV-2 genome. Multiple evidence confirmed that the presence of UTRs enhance the packaging efficiency of infectious virus-like particles (iVLPs) and recruits more nucleocapsid (N) protein, suggesting a critical role in genome compaction and packaging. These insights into the regulatory mechanisms of SARS-CoV-2 genome packaging provide novel targets for antiviral therapeutics and contribute to the broader understanding of coronavirus assembly.

microbiology↗

bioRxiv2024

Mapping HIV-1 RNA Structure, Homodimers, Long-Range Interactions and persistent domains by HiCapR

Human Immunodeficiency Virus (HIV) persists as a leading global health issue. A significant gap in knowledge exists in our understanding of long-range interactions within the HIV-1 RNA genome. To bridge this gap, we introduce HiCapR, incorporating a psoralen crosslinking RNA proximity ligation and post-library hybridization for capturing HIV RNA-RNA interactions. Leveraging HiCapR, we confirm the presence of stem structures in the key regions, such as the 5-untranslated region(5-UTR) and Rev Response Element (RRE) stems, and dimer sites in 5-UTR region, which is responsible for HIV packaging. Importantly, we reveal multiple previously unknown homodimers along the HIV genome, which may have important implications for viral RNA splicing and packaging processes. Also, we uncover a wealth of unprecedented long-range interactions, particularly within the 5-UTR of infected cells. Intriguingly, our findings indicate a pronounced reduction in long-range RNA-RNA interactions, signifying a transition from a state of abundant interactions, hence a relative loose state within infected cells to a condensed structure within virions. Concurrently, we have demonstrated the presence of stable genomic domains within virions that are instrumental in the dimerization process. These domains are preserved throughout the packaging process. Our findings shed light on the functional significance of RNA organization, including stable and persistent genomic domains, homodimerization, and long-range RNA-RNA interactions, in the splicing, packaging as well as assembly of HIV. HighlightsHiCapR is a new proximity ligation method for mapping RNA structures and homodimers in the HIV genome with sufficient reliability and efficiency. Multiple homodimers were discovered along the genome, with potential implications for splicing and packaging processes. Long-range RNA-RNA interactions are abundant in infected cells but significantly reduced in virions. Stable genomic domains encluding homodimer sites are persistent in virions and are involved in dimerization.

genomics↗

bioRxiv2024

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

Alignment against a database of genomes is a fundamental operation in bioinformatics, popularized by BLAST. However, the rate at which microbial genomes are sequenced has continued to increase, and there are now datasets in the millions, far beyond the abilities of existing alignment tools. We introduce LexicMap, a nucleotide sequence alignment tool for efficiently querying moderate length sequences (>250 bp) such as a gene, plasmid or long read against up to millions of prokaryotic genomes. A key innovation is to construct a small set of probe k-mers (e.g. n = 20,000) which are selected to efficiently sample the entire database to be indexed, such that every 250 bp window of each database genome contains multiple seed k-mers each with a shared prefix with one of the probes. Storing these seeds in a hierarchical index enables fast and low-memory alignment. We benchmark both accuracy as the query diverges from the match in the database, and potential to scale to databases of millions of bacterial genomes, showing that LexicMap achieves comparable accuracy with state-of-the-art, but with greater speed and lower memory use. We then benchmark LexicMap on small/diverse (GTDB) and large/redundant (AllTheBacteria and GenBank+RefSeq) databases. Alignment of a single gene against 2.34 million prokaryotic genomes from GenBank and RefSeq takes 3 (rare gene) to 33 (16S rRNA gene) minutes. Full alignment against all bacterial genomes is now possible in minutes with modest resources, supporting querying at scale which will be useful for many biological applications across epidemiology, ecology and evolution. LexicMap produces output in standard formats including that of BLAST and is available under MIT license at https://github.com/shenwei356/LexicMap.

bioinformatics↗

bioRxiv2024

A telosma mosaic virus-based vector for foreign gene expression and virus-induced gene silencing in the perennial woody vine, passion fruit (Passiflora edulis)

Passion fruit (Passiflora edulis) is a perennial, woody, tropical vine crop. It produces edible round to oval fruit that has been increasingly favored for its unique aroma and taste, and richness in antioxidants, vitamins and minerals. However, the functional genomic study of passion fruit lags far behind due to a lack of simple and efficient genetic tools. Here, we report the development of virus-mediated protein overexpression (VOX) and virus-induced gene silencing (VIGS) vector based on telosma mosaic virus (TelMV), an emerging potyvirus infecting passion fruit plants worldwide. This vector, designated pTelMV-GW, incorporates the Gateway-compatible recombination sites for rapid gene cloning. We show that this vector allows for the systemic stable expression of two heterologous proteins, green fluorescent protein (GFP) and bacterial phytoene synthase (crtB) in passion fruit plants, and pTelMV-GW containing different fragments of GFP can also induce systemic gene silencing on the GFP-transgenic N. benthamiana plants. Moreover, we demonstrated that in passion fruit plants, this vector can trigger gene silencing of endogenous phytoene desaturase (PDS) to a limited extent. Furthermore, we upgraded the vector by using a mild TelMV strain that does not induce noticeable symptoms in plants. We show that the upgraded vector (pTelMV-R181K-GW) containing PDS or ChlI fragments induces the robust silencing of the corresponding endogenous gene in passion fruit plants. Together, we reported the first development of VIGS and VOX vectors in passion fruit plants, as the first step in our endeavor to discover horticulturally important genes for improving passion fruit production and quality.

plant biology↗

bioRxiv2024

Molecular architecture of the altered cortical complexity in autism

Autism Spectrum Disorder (ASD) is characterized by difficulties in social interaction, communication challenges, and repetitive behaviors. Despite extensive research, the molecular mechanisms underlying these neurodevelopmental abnormalities remain elusive. We integrated microscale brain gene expression data with macroscale MRI data from 1829 participants, including individuals with ASD and healthy controls, from the Autism Brain Imaging Data Exchange (ABIDE) I and II. Using fractal dimension (FD) as an index for quantifying cortical complexity, we identified significant regional alterations in ASD, within the left temporoparietal, left peripheral visual, right central visual, left somatomotor (including the insula), and left ventral attention networks. Partial least squares (PLS) regression analysis revealed gene sets associated with these cortical complexity changes, enriched for biological functions related to synaptic transmission, synaptic plasticity, mitochondrial dysfunction, and chromatin organization. Cell-specific analyses, protein-protein interaction (PPI) network analysis and gene temporal expression profiling further elucidated the dynamic molecular landscape associated with these alterations. These findings indicate that ASD-related alterations in cortical complexity are closely linked to specific genetic pathways. The combined analysis of neuroimaging and transcriptomic data enhances our understanding of how genetic factors contribute to brain structural changes in ASD.

neuroscience↗

bioRxiv2024

Generation of a biliary tract cancer cell line atlas reveals molecular subtypes and therapeutic targets

Biliary tract cancers (BTCs) are a group of deadly malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we present the integrative analysis of 63 BTC cell lines via multi-omics clustering and genome- scale CRISPR screens, providing a platform to illuminate BTC biology and inform therapeutic development. We identify dependencies broadly enriched in BTC compared to other cancers as well as dependencies selective to the anatomic subtypes. Notably, cholangiocarcinoma cell lines are stratified into distinct lineage subtypes based on biliary or dual biliary/hepatocyte marker signatures, associated with dependency on specific lineage survival factors. Transcriptional analysis of patient specimens demonstrates the prognostic significance of these lineage subtypes. Additionally, we delineate strategies to enhance targeted therapies or to overcome resistance in cell lines with key driver gene mutations. Furthermore, clustering based on dependencies and proteomics data elucidates unexpected functional relationships, including a BTC subgroup with partial squamous differentiation. Thus, this cell line atlas reveals potential therapeutic targets in molecularly defined BTCs, unveils biologically distinct disease subtypes, and offers a vital resource for BTC research.

cancer biology↗

bioRxiv2024

Cell- and state-specific plasticity of striatal glutamatergic synapses is critical to the expression of levodopa-induced dyskinesia

Levodopa-induced dyskinesia (LID) is a debilitating complication of symptomatic therapy in Parkinsons disease (PD). Although there is compelling evidence that striatal pathophysiology is a major driver of LID, the circuit-specific mechanisms contributing to dysfunction remain obscure. This lack of clarity is reflected in the limited options for diminishing established LID. To address this gap, molecular, cellular, and behavioral strategies were used to interrogate striatal indirect pathway spiny projection neurons (iSPNs) in a mouse model of LID. These studies revealed that LID induction led to an up-regulation of GluN2B-containing N-methyl-d-aspartate receptors (NMDARs) specifically at iSPN glutamatergic synapses. This up-regulation was correlated with increased numbers of silent glutamatergic synapses in the hours after levodopa treatment. In this off-state, long-term potentiation (LTP) of iSPN glutamatergic synapses was readily induced and this induction was blocked by antagonists of adenosine type 2 receptors (A2aRs) or GluN2B-containing NMDARs. Systemic administration of the A2aR antagonist tozedenant at the beginning of the off-state significantly reduced the development of LID. More importantly, specifically knocking down the expression of GRIN2B mRNA in iSPNs dramatically attenuated both development and expression of LID, without compromising the beneficial effects of levodopa on movement. Taken together, these studies demonstrate that dyskinesiogenic doses of levodopa trigger cell-specific synaptic adaptations during the off-state that make an important contribution to the network pathophysiology underlying LID and suggest that targeting GluN2B-containing NMDARs in iSPNs could be therapeutically useful.

neuroscience↗

bioRxiv2024

Maternal obesity may disrupt offspring metabolism by inducing oocyte genome hyper-methylation via increased DNMTs

Maternal obesity has deleterious effects on the process of establishing oocyte DNA methylation; yet the underlying mechanisms remain unclear. In the present study, we found that maternal obesity induced by high-fat diet (HFD) disrupted the genomic methylation of oocytes, and that at least a part of the altered DNA methylation was transmitted to the F2 oocytes and the livers via females. We further examined the metabolome of serum and found that the altered metabolites such as melatonin may play a key role in the disrupted genomic methylation in the oocytes of obese mice. We further found that exogenous melatonin treatment significantly reduced the hyper-methylation of HFD oocytes, and the increased expression of DNMT3a and DNMT1 in HFD oocytes was also decreased. To address how melatonin regulates the expression of DNMTs, the function of melatonin was inhibited or activated upon oocytes. Results revealed that melatonin may regulate the expression of DNMTs via the cAMP/PKA/CREB pathway. These results suggest that maternal obesity induces genomic methylation alterations in oocytes, which can be partly transmitted to F2 in females, and that melatonin is involved in regulating the hyper-methylation of HFD oocytes by increasing the expression of DNMTs via the cAMP/PKA/CREB pathway.

developmental biology↗

bioRxiv2024

Leveraging cross-source heterogeneity to improve the performance of bulk gene expression deconvolution

We introduce CSsingle, a novel method that enhances the decomposition of bulk and spatial transcriptomic (ST) data by addressing key challenges in cellular heterogeneity. CSsingle applies cell size correction using ERCC spike-in controls, enabling it to account for variations in RNA content between cell types and achieve accurate bulk data deconvolution. In addition, it enables fine-scale analysis for ST data, advancing our understanding of tissue architecture and cellular interactions, particularly in complex microenvironments. We provide a unified tool for integrating bulk and ST with scRNA-seq data, advancing the study of complex biological systems and disease processes. The benchmark results demonstrate that CSsingle outperforms existing methods in accuracy and robustness. Validation using more than 700 normal and diseased samples from gastroesophageal tissue reveals the predominant presence of mosaic columnar cells (MCCs), which exhibit a gastric and intestinal mosaic phenotype in Barretts esophagus and esophageal adenocarcinoma (EAC), in contrast to their very low detectable levels in esophageal squamous cell carcinoma and normal gastroesophageal tissue. We revealed a dynamic relationship between MCCs and squamous cells during immune checkpoint inhibitors (ICI)-based treatment in EAC patients, suggesting MCC expression signatures as predictive and prognostic markers of immunochemotherapy outcomes. Our findings reveal the critical role of MCC in the treatment of EAC and its potential as a biomarker to predict outcomes of immunochemotherapy, providing insight into tumor epithelial plasticity to guide personalized immunotherapeutic strategies.

bioinformatics↗

bioRxiv2024

Mutating the arginine residue within the FRNK motif of HC-Pro yield highly attenuated strains that confer complete cross protection against telosma mosaic virus (TelMV) in passion fruit (Passiflora edulis)

Telosma mosaic virus (TelMV, Potyvirus, Potyviridae) is an emerging viral pathogen causing a major global threat to passion fruit plantations. However, an efficient strategy for controlling such viruses is not yet available. Cross protection is a phenomenon in which pre-infection of a plant with one virus prevents or delays superinfection with the same or closely related virus. HC-Pro is the potyviral encoded multifunctional protein involved in several steps of viral infection, including multiplication, movement, transmission and RNA silencing suppression. The main hypothesis we tested in this study was whether it is possible to generate attenuated viral strains capable of conferring protection against severe TelMV infection by manipulating the HC-Pro gene. By introducing point mutation into the potyviral conserved motif FRNK of HC-Pro, we have successfully obtained three highly attenuated mutants of TelMV (R181K, R181D and R181E, respectively) that can systemically infect passion fruit plants without any noticeable symptoms. Importantly, these mutants confer complete protection against subsequent infection of severe recombinant virus TelMV-GFP, evidenced by no detection of viral RNA or protein of the superinfection virus in the systemic leaves of passion fruit plants in both early and late stages. Lastly, we demonstrated that the HC-Pros harbored by the highly attenuated mutants exhibited reduced RNA silencing suppression activity in Nicotiana benthamiana leaves. Altogether, this study provides the first demonstration of the generation of highly attenuated strains for TelMV and highlights key amino acid residue involved in complete cross protection against TelMV, opening a new avenue to fight TelMV in the field.

pathology↗

bioRxiv2024

A rapid and efficient in vivo inoculation method for introducing tree stem canker pathogens onto leaves, suitable for large-scale assessment of resistance in poplar breeding progeny

Hybrid breeding, a direct and efficient strategy for disease control and management in tree species, is currently limited by the selection method of resist clones: the "in vitro stem segment inoculation method." This method, constrained by the availability of inoculating materials, cannot rapidly, efficiently, and cost-effectively screen the resistance of all hybrid clones. To overcome these limitations, we introduce a novel pathogen inoculation method for the resistance assessment of hybrid clones in the poplar-Valsa sordida pathosystem. This method involves inoculating the stem canker pathogen on the host leaf, a unique and promising approach we have successfully validated. Results showed that stem canker pathogen V. sordida induced the extended necrotic lesion and even induced the formation of pycnidium structure and conidia on the leaf surface five days after mycelium inoculation; 1) the upper 5-7th leaves exhibited higher resistance than the middle 18-20th leaves; 2) the shading conditions induced more severe symptoms on the leaves than lighting conditions; 3) the juvenile mycelium inoculums (4-day-cultured) were more susceptible to poplar leaves than the old ones (7-day-cultured). Our results demonstrate the robustness of the "in vivo leaf inoculation method" in revealing the resistance differentiation in poplar hybrid clones. According to the leaf necrotic area disease index, we divided these poplar clones into seven different resistance groups. The resistance assessed by leaf assessment was validated in 15 selected poplar clones using the "in vitro stem segment inoculation method." Results showed that the effectiveness of these two methods was consistent. Moreover, the leaf inoculation method can be used to detect the pathogenicity diversity of the pathogen population of tree species. Compared to the conventional "in vitro stem segment inoculation method," the leaf method has the advantages of abundant inoculation materials, easy operation, rapid disease onset, and almost no adverse effect on the host. It is particularly suitable for the resistance screening of all progeny and the early (seedling) phenotypic selection of resistant poplar clones in poplar stem disease resistance breeding. The "in vivo leaf inoculation method" holds significant promise in poplar breeding, tree pathology, and molecular biology research on tree stem diseases.

plant biology↗

bioRxiv2024

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

Spatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms. However, building a robust clustering algorithm to define spatially coherent regions in a single tissue slice, and aligning or integrating multiple tissue slices originating from diverse sources for essential downstream analyses remain challenging. Numerous clustering, alignment, and integration methods have been specifically designed for ST data by leveraging its spatial information. The absence of benchmark studies complicates the selection of methods and future method development. Here we systematically benchmark a variety of state-of-the-art algorithms with a wide range of real and simulated datasets of varying sizes, technologies, species, and complexity. Different experimental metrics and analyses, like adjusted rand index (ARI), uniform manifold approximation and projection (UMAP) visualization, layer-wise and spot-to-spot alignment accuracy, spatial coherence score (SCS), and 3D reconstruction, are meticulously designed to assess method performance as well as data quality. We analyze the strengths and weaknesses of each method using diverse quantitative and qualitative metrics. This analysis leads to a comprehensive recommendation that covers multiple aspects for users. The code used for evaluation is available on GitHub. Additionally, we provide jupyter notebook tutorials and documentation to facilitate the reproduction of all benchmarking results and to support the study of new methods and new datasets (https://benchmarkst-reproducibility.readthedocs.io/en/latest/).

bioinformatics↗

bioRxiv2024

AllTheBacteria - all bacterial genomes assembled, available and searchable

Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not uniformly assembled, quality controlled, annotated or searchable at scale. Here we present AllTheBacteria, an open, community-built resource that transforms public bacterial short-read whole-genome sequencing reads into a uniformly processed discovery platform. The current analysed release contains 2,440,377 high-quality bacterial and archaeal genomes from 11,273 species, together with standardized taxonomic assignments, genome annotations, antimicrobial resistance calls, antiphage-defence annotations, protein structure predictions and AI-ready sequence tables. We show that this infrastructure enables applications that would otherwise be impractical, from global sequence search and outbreak contextualization to pangenome method development, antimicrobial resistance reservoir mapping and antiphage-defence ecology. As a stringent experimental demonstration, we mined 3,919,096 encrypted peptide fragments from AllTheBacteria proteomes using our deep learning model APEX 1.1, identifying 1,867 candidates with predicted antimicrobial activity. We synthesized 24 representative peptides and tested them against 20 clinically relevant bacterial strains, including antibiotic-resistant pathogens. Multiple peptides showed low-micromolar activity, membrane-responsive conformational transitions and selective envelope perturbation. A lead molecule, ATB20, reduced Acinetobacter baumannii burden in a murine skin abscess model with efficacy comparable to polymyxin B and no overt toxicity. Together, these results establish AllTheBacteria as both a foundational community resource for microbiology and a renewable engine for AI-guided antimicrobial discovery.

bioinformatics↗

bioRxiv2024

PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets

Designing protein-binding proteins is critical for drug discovery. However, the AI-based design of such proteins is challenging due to the complexity of ligand-protein interactions, the flexibility of ligand molecules and amino acid side chains, and sequence-structure dependencies. We introduce PocketGen, a deep generative model that simultaneously produces both the residue sequence and atomic structure of the protein regions where ligand interactions occur. PocketGen ensures consistency between sequence and structure by using a graph transformer for structural encoding and a sequence refinement module based on a protein language model. The bilevel graph transformer captures interactions at multiple scales, including atom, residue, and ligand levels. To enhance sequence refinement, PocketGen integrates a structural adapter into the protein language model, ensuring that structure-based predictions align with sequence-based predictions. PocketGen can generate high-fidelity protein pockets with superior binding affinity and structural validity. It operates ten times faster than physics-based methods and achieves a 95% success rate, defined as the percentage of generated pockets with higher binding affinity than reference pockets. Additionally, it attains an amino acid recovery rate exceeding 64%.

bioinformatics↗

bioRxiv2024

Integrated multi-omics analysis of Klebsiella pneumoniae revealed the discrepancy in flavonoid effect against strain growth between Rutin and Luteolin

The emergence of drug resistant pathogenic bacteria is increasingly challenging conventional antibiotics. Plant derived flavonoids are always considered as potential alternatives to antibiotics due to their antimicrobial properties. However, the molecular mechanisms by which flavonoids inhibit pathogenic microorganisms growth are not fully understood. In order to better understand the inhibitory mechanism of flavonoids, two flavonoids were used to incubate Klebsiella pneumoniae ATCC700603. After incubation for 4 hours, both the metabolomic and transcriptomic analysis were performed. In present study, 5,483 genes and 882 metabolites were measured. Compared to wild control, the Rutin and Luteolin induced 507 and 374 differentially expressed genes (DEGs), respectively. However, the number of differential abundant metabolites (DAMs) were the same. The correlation between DEGs and DAMs were studied. The top 10 correlated DEGs and DAMs were identified in each comparative groups. Our results showed that, compared to Luteolin, Rutin induced the accumulation of metabolites and suppressed genes expression. Our results provided an explanation for the disparate effects of two flavonoids and demonstrated the inhibitory mechanism of Rutin on strain growth.

bioinformatics↗

bioRxiv2024

An Engineered IGF2 Mutant for Lysosomal Targeting Chimeras Development and Membrane Proteins Degradation

Lysosome-targeting chimeras (LYTACs) have emerged as a promising strategy for targeted degradation of membrane proteins, offering potential applications in drug development. Currently, two main methods for developing LYTACs exist: chemically modified antibodies [1-2] and wild-type insulin-like growth factor 2 (IGF2) fusion proteins (iLYTACs) [3]. However, the fusion of the IGF2 arm within iLYTACs carries the risk of activating IGF1R tyrosine kinase activity and promoting tumor development. To address this concern, we introduce eiLYTACs, a technology that employs engineered IGF2 fusion antibodies to induce degradation of endogenous membrane proteins. Compared to the wild-type IGF2, the engineered IGF2 mutant exhibited minimal binding affinity for IGF1R but demonstrated a significant 100-fold increase in its binding affinity for IGF2R. In contrast to wild-type IGF2, which promotes tumor growth, the cells incubated with the engineered IGF2 showed no stimulation of tumor growth. The eiLYTACs strategy effectively inhibits tumor cell proliferation by degrading specific targets, resulting in a significant reduction in xenograft tumor size in experimental nude mice. More interestingly, our research revealed that eiLYTACs simultaneously degrade both homo- and heterodimers of disease-relevant proteins,which offer a promising strategy to address the activation of compensatory bypass signaling pathways, drug resistance, and tumor heterogeneity.

biochemistry↗

bioRxiv2024

Identification and characterization of a temperature sensitive chlorotic soybean mutant

Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "vir1" phenotype results in smaller stature, weaker stems, and a smaller root system with smaller nodules. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate mutation, a single-base change in Glyma.07G102300 that disrupts splicing of the second intron. Single cell transcriptomic profiling indicates that this gene is expressed primarily in mesophyll cells and RNA sequencing data indicates it is upregulated in germinating seedlings by cold stress. Previous studies have shown that mutations to Os05g34040, the rice homolog of Glyma.07G102300, produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing soybean vir1 mutants at lower temperatures also resulted in a more severe phenotype. In addition, transgenic expression of wild type Glyma.07G102300 in the knockout mutant of the Arabidopsis homolog At4930720 rescues the chlorotic phenotype, further supporting the hypothesis that the mutation in Glyma.07G102300 is causal of the vir1 phenotype.

plant biology↗

bioRxiv2023

Virus-induced gene silencing (VIGS) as a tool for functional genetic analysis in passion fruit plants

Passion fruit (Passiflora edulis) is grown perennially in sub-tropical and tropical areas. Its fruits contain multiple vitamins and antioxidants, and thus are consumed increasingly in drinks and foods. However, the functions and regulations of genes that are engaged in the biosynthesis of the health-promoting compounds in passion fruits remain largely unknown. Its whole genome sequence has just been published recently. Virus-induced gene silencing (VIGS) is a reverse genetics tool for analyzing gene function. Here, we engineered telosma mosaic virus (TelMV), a potyvirus infecting passion fruit, into a VIGS vector by inserting the Gateway-compatible recombination sites. The newly constructed TelMV-VIGS virus successfully expressed foreign protein and induced systemic infection in both Nicotiana benthamiana and P. edulis plants. Intriguingly, TelMV-VIGS vector containing different fragments of green fluorescent protein (GFP) gene induced systemic gene silencing on the GFP-transgenic N. benthamiana plants (16c). When the phytoene desaturase (PDS) gene, an endogenous gene in passion fruit, was engineered into the vector, it triggered the silencing of PePDS, as evidenced by the reduced mRNA levels and photobleached phenotype. We reported the first development of VIGS vector in passion fruit, as the first step in our endeavor of discovering horticulturally important genes for improving passion fruit production and quality.

plant biology↗