Integrated transcriptome and translatome analyses reveal the early regulatory network of Brassica napus roots in response to the growth-promoting rhizobacterium Pseudomonas simiae WCS417

Integrated transcriptome and translatome analyses reveal the early regulatory network of Brassica napus roots in response to the growth-promoting rhizobacterium Pseudomonas simiae WCS417 | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Integrated transcriptome and translatome analyses reveal the early regulatory network of Brassica napus roots in response to the growth-promoting rhizobacterium Pseudomonas simiae WCS417 Li Zhang, Jie Liu, Zhipeng Zhou, Wei Wang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7990582/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 12 Jan, 2026 Read the published version in Molecular Breeding → Version 1 posted 9 You are reading this latest preprint version Abstract Interactions between plant roots and complex microbial communities are critical for plant environmental adaptation. Pseudomonas simiae WCS417, a Gram-negative plant growth-promoting rhizobacterium (PGPR), is a model organism in plant-microbe interaction research and featured in over 750 studies since the 1990s. However, the translatome dynamics induced by WCS417 remain poorly understood. This study employed an integrated multi-omics approach, combining transcriptome (RNA-seq) and translatome (RNC-seq) analyses, to systematically investigate the transcriptional and translational regulatory networks in Brassica napus roots during early colonization by WCS417. Our results demonstrate that WCS417 significantly promotes lateral root formation, suppresses primary root elongation, and increases plant biomass. At the molecular level, WCS417 inoculation triggered extensive changes in gene expression and translation at 30 minutes and 6 hours post-inoculation, affecting key processes including phytohormone signaling, cell wall remodeling, immune responses, and abiotic stress adaptation. Notably, although transcript levels of some immune-related genes were downregulated, their translation efficiency was significantly enhanced, suggesting that plants maintain basal immunity while facilitating symbiotic establishment. Furthermore, WCS417 dynamically regulated genes involved in nitrogen/phosphorus uptake and core low-temperature response transcription factors in Brassica napus roots. These findings reveal a multi-layered regulatory mechanism by which WCS417 optimizes root system architecture and balances immunity with growth in Brassica napus , providing new insights into plant-microbe interactions. Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Introduction Plants, as immobile organisms, have their roots constantly exposed to a highly complex soil microbial environment comprising diverse microbial communities, including beneficial, pathogenic, and commensal microorganisms (Yu et al. 2019b ). These microbial interactions have significant impacts on plant growth, development, immune responses, and environmental adaptation. To survive under such dynamic conditions, plants have evolved complex adaptive strategies, among which the selective recruitment of beneficial microbes stands out as a critical mechanism (Zhang et al. 2023 ; Wang and Song 2022 ). This process involves the modulation of root morphology and physiological traits in response to microbial stimuli (Vacheron et al. 2018 ; Contreras-Cornejo et al. 2009 ). Central to plant-microbe interactions is the recognition of microbe-associated molecular patterns (MAMPs), which trigger precise developmental reprogramming to facilitate symbiotic associations (Hacquard et al. 2017 ; Stringlis et al. 2018 ). Notably, these interactions induce dynamic remodeling of root architecture, characterized by the suppression of primary root elongation and the stimulation of lateral root proliferation. Such structural modifications ultimately enhance the plant’s capacity for resource acquisition, thereby optimizing water and nutrient uptake efficiency (Vacheron et al. 2018 ; Motte et al. 2019 ; Koevoets et al. 2016 ). Since its isolation from wheat roots in 1988, Pseudomonas simine WCS417 has been recognized as an important plant growth-promoting rhizobacterium (PGPR) (Pieterse et al. 2020 ). It effectively suppresses soil-borne diseases caused by fungi, bacteria, and nematodes, such as take-all and Fusarium wilt, while also enhancing tolerance to abiotic stresses, including drought and salinity (Nel et al. 2006 ; Canchignia et al. 2017 ; M. Leeman and Schippers 1996; Ran et al. 2005 ). To date, it has been extensively studied and validated in more than 750 research studies (Pieterse et al. 2020 ), while the effect of WCS417 on B. napus has not been investigated to date. WCS417 has been shown to markedly alter root system architecture, thereby improving water and nutrient uptake efficiency in many plant species (Aparicio et al. 2025 ; Zhou et al. 2025 ; Stringlis et al. 2018 ). In model plants such as Arabidopsis thaliana , WCS417 colonization induces profound remodeling of root architecture, such as inhibition of primary root elongation, enhanced lateral root formation, and promotion of root hair development (Stringlis et al. 2018 ). These morphological alterations are orchestrated through complex interactions with auxin signaling pathways (Zamioudis et al. 2013 ). Mechanistic studies reveal that WCS417 employs multiple synergistic strategies to influence plant growth. First, the bacterium synthesizes phytohormone, such as indole-3-acetic acid (IAA), which modulates the expression of auxin response factors (ARFs) to regulate the initiation and development of lateral root primordia (Zamioudis et al. 2013 ). Second, volatile organic compounds (VOCs) produced by WCS417 induce the expression of root-specific transcription factor MYB72 to regulate root development (Zamioudis et al. 2015 ; Zamioudis et al. 2014 ). Furthermore, both VOCs and microbial siderophores produced by WCS417 activate the MYB72-FIT1 signaling module, upregulating the expression of iron acquisition genes ( FRO2 and IRT1 ), thereby improving plant iron nutrition (Verbon et al. 2019 ; Verbon et al. 2017 ). Additionally, WCS417 secretions specifically regulate the expression of sugar transporter proteins (SWEET11 and SWEET12), suggesting a sophisticated mechanism for optimizing carbon allocation during symbiotic interactions (Desrut et al. 2020 ). In plant roots, translational regulation serves as a critical mechanism of protein expression control that is not only involved in nutrient uptake, developmental processes, and adaptation to abiotic stress, but also plays a central role in root-microbe interactions (Li et al. 2024 ; Yang et al. 2025 ; Shang et al. 2025 ; Du et al. 2025 ; Wu et al. 2024 ). Recently developed protoplast-free single-nucleus RNA sequencing (snRNA-seq) has revealed that roots employ spatially partitioned and cell type-specific translational strategies to accurately distinguish beneficial from pathogenic microbes, maintain microbiome homeostasis, and coordinate immune responses. (Yang et al. 2025 ; Long et al. 2021 ). In the root meristematic zone, beneficial microbes significantly upregulate the expression of translation-related genes and promote the accumulation of ribosomal proteins and translation factors, thereby facilitating microbe-mediated growth promotion. In contrast, the mature zone employs localized translational mechanisms to activate immune responses, enabling rapid synthesis of defense-related proteins, including those involved in triterpenoid biosynthesis, to counteract pathogen invasion (Yang et al. 2025 ). This spatially specialized translatability allows the root system to simultaneously promote beneficial symbiosis and effectively suppress harmful infections. Recent advances in cell type-specific ribosome profiling have further elucidated the spatial heterogeneity of translational dynamics in different root zones upon microbial contact, highlighting the key role of translational regulation in root-microbe interactions (Froschel et al. 2021 ; Liu et al. 2022 ). Thus, by precisely controlling the spatiotemporal production of proteins, translational regulation emerges as a core mechanism underlying root-microbial symbiosis, immune balance, and environmental adaptation. Brassica napus ( B. napus ) is one of the most important oilseed crops worldwide. However, whether WCS417 could regulate root development and disease resistance in B. napus remains largely uninvestigated. Furthermore, although translational regulation is critical for microbe-root interactions, systematic studies of the root translatome, particularly the molecular mechanisms underlying transient translational responses of plants during early colonization, remain relatively limited. In this study, we employed an integrated multi-omics approach, combining RNA-seq and RNC-seq (Ribosome Nascent-chain Complex sequencing) to systematically investigate the regulatory networks orchestrated by WCS417 at both transcriptional and translational levels during early colonization of B. napus roots. Method Plant material and growth conditions Brassica napus seeds were surface sterilized with 75% ethanol for 8–10 min, followed by 50% bleach for another 2 min, and then washed three times with sterilized water. Afterward, seeds were germinated on ½ Murashige and Skoog (MS) agar plates with 0.5% sucrose in a growth chamber (22°C under a 16 h light/8 h dark period with light intensity at 450 µmolm − 2 s − 1 ) for 2 days. For measurement of plant biomass, Seedlings were transferred to ½ MS agar plates or natural soil, and then plants were grown at 21°C growth room under a 16 h light/8 h dark period with light intensity at 450 µmolm − 2 s − 1 . For the RNC-seq, seedlings were grown in liquid ½ MS medium containing 2% (w/v) sucrose for 10 days (16 h Light/8 h Dark) and transferred to fresh liquid ½ MS medium without sucrose for 2 more days before inoculation. Cultivation of Pseudomonas simiae WCS417 and treatment Pseudomonas simiae WCS417 was cultured at 28°C on LB agar plates supplemented with 50 µg mL − 1 of rifampicin. After 24 h of growth, cells were collected in 10 mM MgCl 2 , washed twice with 10 mM MgCl 2 by centrifugation for 5 min at 5000 g, and finally resuspended in ddH 2 O. For RNC-seq, WCS417 was diluted to OD600 = 0.5 in 10mM MgCl 2 and then added to the liquid rhizosphere to a final OD600 of 0.05. Liquid ½ MS medium supplemented with an equal volume of 10mM MgCl 2 was used as a mock control. Measurement of plant biomass and parameters of root architecture For treatment with live WCS417 cells, Brassica napus seedlings were germinated on ½ MS agar plates with 1% sucrose. two-day‐old Brassica napus seedlings were transferred to new agar‐solidified ½ MS plates with 1% sucrose with or without WCS417 (final concentration OD 600 = 0.0005). Ten days after the start of the treatments, shoot fresh weight, primary root length, number of lateral roots, and hypocotyl length were determined. Ribosome-nascent chain complex (RNC) extraction RNC extraction was performed as previously described (Wang et al. 2013 ). with minor modifications. Briefly, roots were ground using a pre-chilled mortar with the addition of 2 mL of cell lysis buffer (200 mM Tris–HCl, pH 7.4, 35 mM MgCl₂, 200 mM KCl, 100 µg/mL cycloheximide, and 1% Triton X-100). After incubation on ice for 30 min, the lysates were centrifuged at 16,200 g for 20 min at 4°C. The supernatants were then layered onto 0.4 mL of a sucrose cushion buffer (1.75 M sucrose in gradient buffer). RNCs were pelleted by ultracentrifugation at 256,000 g for 3 h at 4°C (Merchante et al. 2016 ). RNA-seq The sequencing libraries were constructed following the Fast RNA-seq Lib Prep Kit V2 (ABclonal, #RK20306). Briefly, total RNA was isolated using TRNzol (TIANGEN, #DP424). Then, 1 µg of total RNA or RNC-mRNA was subjected to the polyA + mRNA isolation using the Poly(A) mRNA Capture Module beads (ABclonal, #RK20340) following the manufacturer’s instructions. The mRNA was fragmented at 94°C for 15 min to obtain 200–250 bp inserts. First-strand cDNA was synthesized by First Strand Synthesis Enzyme Mix, and double-stranded cDNA was synthesized by Second Strand Master Mix using Second Strand & dA Buffer with dUTP *. The adapters were ligated by Ligase Mix T5. Ligated dscDNAs were purified and then amplified by 16 cycles of PCR with 2x PCR Master Mix and purified using AFTMag NGS DNA Clean Beads (ABclonal, #RK20257). Purified libraries were quantified by Qubit® 2.0 Fluorometer (Thermo Fisher, #Q33238). Libraries were barcoded, pooled, and sequenced in a HiSeq 2000 or 2500 machine (Paired-end 150-bp). High-quality reads that passed the Illumina quality filters were kept for the sequence analysis (Supplementary Table S1 ). Data analysis Both RNA-Seq and RNC-Seq reads were first processed using fastp (v1.01) to remove adapter sequences (Chen 2025 ). The resulting clean reads were then aligned to reference sequences of rRNA, tRNA, and other non-coding RNAs of B. napus , obtained from the Ensembl database, using Bowtie2 (v2.5.4) (Dyer et al. 2025 ; Langmead and Salzberg 2012 ) to eliminate the contaminations. Subsequently, the filtered RNA-Seq and RNC-Seq reads were mapped to the B. napus reference genome (ZS11 v0), downloaded from the BnIR database, using STAR (v2.7.11b) (Song et al. 2020 ; Yang et al. 2023 ; Dobin et al. 2013 ). Gene expression quantification was performed using the featureCounts tool within the Subread package (v2.0.2) (Liao et al. 2013 ). Quality assessment of the processed datasets, including principal component analysis (PCA), enzymatic bias evaluation, gene coverage analysis, and sample reproducibility, was carried out using RiboShiny (v0.1), an integrated platform designed for comprehensive translation data analysis and visualization (Ren et al. 2025 ). To identify differentially expressed genes (DEGs), the DESeq2 package (v1.4) in R was applied using the likelihood ratio test, followed by shrinkage of log2 fold changes (LFC) via the lfcShrink function with the ashr estimator (Love et al. 2014 ). Genes with an adjusted p -value (Padj) < 0.05 and |log₂(LFC)| ≥ 0.585 were classified as differentially transcriptionally regulated. Translation ratios (TR) and differentially translated genes (DTRGs) were identified using the RiboShiny (v0.1) pipeline. Gene Ontology (GO) enrichment analysis for both DEGs and DTEGs was performed using the BnIR database, with a minimum count threshold of five genes per category. Results Developmental responses of B. napus seedlings to WCS417 In this study, B. napus cultivar Zhongshuang 11 (hereafter ZS11) was used to investigate the effects of WCS417 colonization on plant development. Two-day-old ZS11 seedlings were transferred to a ½ MS plate with or without WCS417 suspension. After 10 days of incubation in the greenhouse, the growth of ZS11 seedlings with or without WCS417 treatment was examined. We found that there is a 3.18-fold increase in lateral root number and a 50.1 ± 2.5% reduction in primary root length in the WCS417-treated seedlings compared with the control (Fig. 1 A-C, Fig. S1 ). In addition, WCS417 inoculation led to significant increases in both root (35.9 ± 9.4%) and shoot (43.5 ± 7.9%) fresh weight (Fig. 1 D-E, Fig. S1 ). These results align with earlier findings by Zamioudis et al. ( 2013 ) on WCS417-induced architectural remodeling in Arabidopsis thaliana , suggesting an evolutionary conservation of this PGPR’s growth-promoting property within the Brassicaceae family (Zamioudis et al. 2013 ). WCS417 induces a transient boost in global translation in rapeseed roots during early colonization WCS417 colonization inhibits primary root growth, promotes lateral root development, and increases both roots and shoots biomass in B. napus . These phenotypic changes align with prior observations in model plants, such as Arabidopsis thaliana (Zamioudis et al. 2013 ). Although the mechanisms regulating WCS417-mediated root development and growth have been extensively characterized in earlier studies, the translational regulatory mechanisms triggered by its colonization of host roots, particularly the transient translational responses during early colonization, remain poorly understood. To investigate the early translational response of rapeseed roots to Pseudomonas simiae WCS417, we performed polysome profiling at 30 minutes and 6 hours post-inoculation (He et al. 2024 ). The results demonstrated a significant increase in the polysome-to-monosome (P/M) ratio at both time points compared to the control, indicating a marked enhancement of global translational activity. Notably, the comparable P/M ratios between the 30-minute and 6-hour samples suggest that this heightened translational state is rapidly established and maintained during early colonization, rather than representing a fleeting response. RNA-seq and RNC-seq Quality Control Analysis To investigate the role of translational regulation during early WCS417 colonization in root development, we performed an integrated analysis of transcriptome (RNA-seq) and translatome (RNC-seq) profiles. Two-day-old ZS11 seedlings were transplanted into liquid ½ MS medium supplemented with 2% sucrose and grown in the greenhouse for 12 days. Seedlings were then treated with a bacterial suspension of WCS417 at OD₆₀₀ = 0.05 for either 30 minutes or 6 hours. Each biological replicate consisted of root tissues pooled from 5–7 seedlings, with two independent replicates per condition. The collected samples were subjected to cell lysis, ribosome isolation, and extraction of ribosome-protected mRNA fragments. Subsequently, corresponding RNA-seq and RNC-seq libraries were constructed for each sample using commercial kits, followed by high-throughput sequencing for transcriptomic and translatomic analysis. Stringent quality control procedures were applied to the raw sequencing data. Each sample yielded more than 34 million raw reads, with Q30 scores exceeding 94%. No adapter contamination or abnormal GC content was detected based on assessments with FastQC and MultiQC. High-quality reads were aligned to the ZS11 reference genome using STAR, with a median unique mapping rate of 80%. Gene coverage uniformity was high without notable 3’ bias, indicating high RNA integrity and library preparation quality. Collectively, these results confirm that the sequencing data are of high quality and suitable for subsequent analysis. After verifying library quality, we further evaluated the reliability of the RNA-seq and RNC-seq data. Inter-sample correlation analysis showed that the correlation coefficients among biological replicates within each group (control, 30-minute, and 6-hour treatments) were close to 1, indicating high intra-group reproducibility, while clear differences were observed between groups (Fig. S2 C). Principal component analysis (PCA) further confirmed clear separation between control and treatment groups in the principal component space, demonstrating high reliability of the transcriptome data (Fig. S2 D). Pearson correlation heatmaps of RNA-seq and RNC-seq data across the three time points revealed substantial changes in gene expression patterns following WCS417 inoculation. PCA results indicated that transcriptional and translational alterations occurred as early as 30 minutes after inoculation, with more pronounced changes at 6 hours after inoculation (Fig. S2 D), suggesting that these responses are likely induced by WCS417 colonization. WCS417 modulates multiple physiological processes in B. napus roots during early colonization To systematically investigate changes in gene expression, we performed differential expression analysis at both the transcriptome and translatome levels across all time points after normalization (Fig. 3 , Table S1 ). Scatter plots comprehensively display the distribution of differentially expressed genes (DGEs) and differentially translated genes (DTGs) for each comparison group, including WCS417 treatment for 30 minutes versus control, 6 hours versus control, and 6 hours versus 30 minutes. Transcriptome analysis revealed that compared to the control, WCS417 treatment for 30 minutes induced up-regulation of 1,806 genes and down-regulation of 1,117 genes; after 6 hours of treatment, the numbers of up- and down-regulated genes were 2,328 and 2,907, respectively; while the comparison between the 6-hour and 30-minute treatment groups identified 2106 up-regulated and 3100 down-regulated genes. At the translatome level, WCS417 treatment for 30 minutes versus control resulted in 1,762 up-regulated and 1,628 down-regulated genes; after 6 hours, 1,699 and 1,914 genes were up- and down-regulated, respectively; and the comparison between the two treatment time points showed 1,659 up-regulated and 2,645 down-regulated genes. Overall, WCS417 treatment induced extensive transcriptional and translational responses in the roots as early as 30 minutes, with the number of affected genes further increasing at 6 hours (Fig. 3 , Table S2 - S3 ). In the analysis of DEGs and DTGs, genes related to plant growth, development, and nutrient uptake were significantly affected. Genes associated with lateral root development (e.g., CLE1 and WOX11 ) (Nakagami et al. 2023 ; Ge et al. 2019 ) were upregulated in response to WCS417 (Fig. 3 ), which is consistent with the phenotype that WCS417 promotes lateral root formation in B. napus (Fig. 1 A). On the other side, homologs of PXMT1 , which could promote primary root elongation (Chung et al. 2016 ), were firstly upregulated at 30 mins of WCS417 treatment, but significantly downregulated at both transcriptional and translational levels at 6 hours of WCS417 treatment (Fig. 3 ), which is in line with the long term suppression of primary root elongation by WCS417 (Fig. 1 B). Concurrently, notable changes were detected in genes related to nutrient absorption. The expression and translation of several homologs of NRT2 , a high-affinity nitrate transporter involved in nitrogen uptake (Jacquot et al. 2020 ), were significantly upregulated 6 hours after inoculation. Meanwhile, the expression and translation of PHT3 homologs, which encode phosphate transporters (Mlodzinska and Zboinska 2016 ), also increased 6 hours after WCS417 inoculation. These results indicate that WCS417 colonization may enhance nitrogen and phosphate utilization and thereby promote plant growth (Fig. 1 C, Fig. 3 ). In addition to growth and development-related genes, WCS417 treatment significantly affects the expression of many abiotic stress-related genes. Genes associated with antioxidant, drought, and salt stress responses (e.g., ERF53 , ERF54 , and OXS3 ) exhibited elevated transcriptional and translational activity at both 30 minutes and 6 hours. The expression of GAS2 , an enzyme catabolizing ABA to phaseic acid (PA) and putative 8’-carboxy-ABA (Lange et al. 2023 ), was consistently elevated at both time points. Interestingly, the expression of DREB1B, DREB1C, DREB1D , and DREB1E (Fowler et al. 2005 ; Vyse et al. 2022 ), core AP2/ERF family transcription factors in the low-temperature response pathway, was consistently reduced at both time points (Fig. 3 ). The function of these TFs in plant-microbe interaction was largely unexplored and worth further investigation. WCS417 infection also dynamically modulated the expression of immune-related genes. For instance, positive immune regulators such as SEN1 (which acts downstream of the SA and JA signaling pathways) (Schenk et al. 2005 ) and CBL7 (a calcium sensor involved in immune signal transduction) (Perez-Alonso et al. 2022 ) were consistently up-regulated at both the transcriptional and translational levels at the two time points examined, indicating that transient WCS417 infection activates plant immune responses. In contrast, the expression of CYP94B1 , a negative regulator of JA signaling (Bruckhoff et al. 2016 ), was up-regulated at 30 minutes post-infection but down-regulated at 6 hours (Fig. 3 ). This expression pattern may help to alleviate the suppression of immune responses at later stages, thereby preventing excessive immune activation and facilitating a balance between growth and defense. In summary, these results demonstrate that during early colonization, WCS417 modulates multiple physiological processes, contributing to the rebalancing of plant immunity and development. WCS417 modulates immune responses in B. napus roots during early colonization To further elucidate the regulatory patterns of gene expression during the symbiotic interaction between WCS417 and B. napus roots, we performed Gene Ontology (GO) enrichment analysis on the differentially expressed genes (Fig. 4 , Table S4 - S5 ). The results indicated that both the transcriptomic and translatomic data were significantly enriched in pathways related to immune response, root development, hormone signaling, and amino acid transport during WCS417 infection, with the notable observation that several pathways enriched in the RNC-seq data (such as the jasmonic acid-mediated signaling pathway) were also detected in the RNA-seq data, suggesting a coordinated regulatory process from transcription to translation. Previous studies have indicated that although WCS417 is a non-pathogenic bacterium, its interaction with plant roots can still activate certain immune-related signaling pathways (Ruan et al. 2019 ; Hou and Tsuda 2022 ; Huang et al. 2016 ; van Loon et al. 2006 ; Janda et al. 2020 ; Kachroo et al. 2020 ; Miao et al. 2025 ; Shidore and Triplett 2017 ; Hacquard et al. 2017 ). Our results demonstrate that at the early stage of WCS417 inoculation (30 minutes), GO terms related to salicylic acid (SA), jasmonic acid (JA) signaling pathways were significantly upregulated (Fig. 4 A-B). As core components of the plant defense system, these pathways are known to comprehensively regulate immune responses (Mao et al. 2007 ; Hofmann et al. 2006 ; Vorwerk et al. 2007 ; Yang et al. 2020 ). At the gene expression level, biosynthesis-related genes in the SA pathway (such as WRKY28 ) and the JA pathway (such as AOC2 , LOX3 , and LOX4 ) showed consistent upregulation at both transcriptional and translational levels (Fig. 3 – 4 ). These findings suggest that although WCS417 is a beneficial rhizobacterium, its initial colonization triggers an immune response in the plant, thereby inducing defense mechanisms to counteract WCS417 invasion. In the GO enrichment analysis conducted at 6 hours post-WCS417 infection and in comparison with the 30-minute time point, immune-related responses, including the JA and ET signaling pathways (e.g., LOX3 , LOX4 , PDF1.4 , ERF1A , ERF12 , ERF13 ), exhibited a gradual downregulation trend (Chandler and Werr 2020 ; Yang et al. 2020 ) (Fig. 3 - 4 B). This shift suggests a potential transition of the plant from a defensive state toward symbiotic adaptation. Notably, at 30 minutes post-inoculation, the transcription factor ERF018 , which regulates JA biosynthesis, was already significantly downregulated at both transcriptional and translational levels (Huang et al. 2021 ) (Fig. 3 ). This observation implies that JA biosynthesis-related genes may be initially modulated at the translational level to fine-tune the immune response, followed by subsequent transcriptional and translational regulation of JA synthesis-related genes by 6 hours post-infection. Concurrently, genes associated with processes critical for symbiosis were upregulated at both transcriptional and translational levels. These included genes involved in cell wall remodeling (e.g., EXPA1 , EXPA10 , EXPA15 ), root development (e.g., EP3, SMB, CLE1 ), amino acid transport (e.g., GDU6 , GDU1 , LHT1 ), and auxin biosynthesis (e.g., YUC6, WEI8 ) (Cha et al. 2015 ; Fang et al. 2016 ; Jacquot et al. 2020 ; Nakagami et al. 2023 ; Nakano et al. 2011 ; Pratelli et al. 2010 ; Tao et al. 2024 ; Wang et al. 2022 ) (Fig. 3 - 4 B). These changes suggest that the plant promotes root structural reorganization and hormonal responses to accommodate WCS417 colonization. To systematically investigate the coordinated and stage-specific regulation of transcription and translation across different time points, we employed UpSet plots to analyze gene sets that were either commonly or uniquely responsive at each time point (Fig. 5 A-B). The results revealed a substantial number of differentially expressed genes (DEGs) shared between the two time points at both transcriptional and translational levels. These common DEGs likely represent a persistent and core response essential for the interaction, potentially forming a “core response module” critical for the establishment of symbiosis. In addition, each treatment group contained genes that were specifically co-regulated at the transcriptional and translational levels in a time-dependent manner, as well as genes altered exclusively at either level. This pattern indicates that distinct physiological processes are regulated at different stages, highlighting the dynamic and phase-specific nature of the host response during WCS417 colonization. Furthermore, the presence of independent transcriptional and translational DEG sets in the UpSet plot suggests that WCS417 treatment induces an imbalance between transcription and translation for a subset of root genes. To further dissect the coordination between transcriptional and translational regulation, we generated a nine-quadrant scatter plot based on transcript-level changes and translational-level changes (Fig. 5 C-E). Differential expression analysis was performed using DESeq2, and genes with an adjusted p -value > 0.05 were excluded. The results showed that during WCS417 colonization from 30 minutes to 6 hours, most genes exhibited consistent trends in both transcriptional and translational changes, indicating a coordinated regulatory mode (Fig. 5 C-E). However, a subset of genes displayed different changes, with misaligned mRNA expression and translation levels, some even showing opposite trends (e.g., upregulated mRNA with decreased translation, or downregulated mRNA accompanied by enhanced translation). These genes are likely subject to post-transcriptional regulation, suggesting that WCS417 infection specifically modulates the translation efficiency of certain genes. WCS417 fine-tunes the translational ratios of immune and root development genes . To further elucidate the regulatory impact of WCS417 on translational control in B . napus roots, we compared translation ratios (TR) between untreated controls and roots treated for 30 minutes and 6 hours. After 30 minutes of WCS417 treatment, 3,223 genes exhibited significant changes in TR, with 3,021 exhibiting increased ratios and 202 showing decreased ratios, indicating that extensive translatome reprogramming had already occurred during the early inoculation stage, suggesting a critical role of translational regulation in the initial establishment of symbiosis (Fig. 6 A, Table S6 ). After 6 hours of treatment, the number of genes with altered TR declined to 1,486, of which 1,006 showed elevated TR and 480 showed reduced TR, reflecting a more convergent translational response as the host adapted to bacterial colonization (Fig. 6 B, Table S6 ). Notably, comparison with the 30-minute treatment group revealed TR alterations in 2,061 genes at the 6-hour time point, with 772 genes exhibiting increased TR and 1,289 showing decreased TR (Fig. 6 C, Table S6 ). These genes are likely involved in maintaining cellular homeostasis or executing core regulatory functions during sustained symbiosis. Collectively, these results demonstrate that WCS417 infection triggers dynamic reprogramming of translation efficiency. Differential translation ratios (DTR) analysis revealed that WCS417 colonization triggers extensive translatome reprogramming during early infection. At 30 minutes post-inoculation, the TR of multiple immune-related genes (e.g., CRK11 , HA5 , GR2 , ZRK10 , and TIFY6B ) was significantly elevated, indicating rapid activation of host immune responses upon initial contact (Chen et al. 2003 ; Zhao et al. 2022 ; Zarei et al. 2017 ; Diplock et al. 2023 ). Concurrently, increased TR of cell wall-related factors MYB54 and PME5 suggested that cell wall remodeling represents an early physiological adaptation to bacterial colonization (Zhong et al. 2008 ; Etchells et al. 2012 ) (Fig. 6 A). As colonization progressed to 6 hours, the TR of ERF13 (Yu et al. 2024 ), a key transcription factor in the JA/ET signaling pathway, was consistently suppressed, while the immune negative regulator HA5 and TIFY6B showed enhanced TR, implying that plants may selectively suppress certain immune pathways to facilitate symbiotic establishment (Chini et al. 2007 ). Furthermore, significantly increased TR of the endoplasmic reticulum formation-related gene BGLU18 and the amino acid transporter CAT5 at 6 hours suggested reinforced secretory capacity and nitrogen utilization to support host-microbe interface formation (Bizan et al. 2025 ; Su et al. 2004 ) (Fig. 6 B). In the 6-hour versus 30-minute comparison, sustained elevation in TR was observed for the phosphate transporter PHT4 (Cubero et al. 2009 ), root development-related gene DOT4 (Petricka et al. 2008 ), and the sucrose efflux transporter SWEET15 (Desrut et al. 2020 ), further supporting the role of WCS417 in enhancing nutrient acquisition and root development. Notably, tRNA methyltransferases TRM8b and TRM4B , which are critical for tRNA stability, proper folding, and overall translational accuracy, also exhibited significantly increased TR (Fig. 6 C). Their upregulation may systemically enhance global protein synthesis capacity during microbial colonization. To assess systematic differences in TR across treatment groups, we first visualized the overall TR distribution using empirical cumulative distribution function (ECDF) curves and boxplots (Fig. S3 ). The results showed that compared to the control group, both the 30-minute and 6-hour treatment groups exhibited significantly higher overall TR levels, displaying a dynamic trend of initial increase followed by a slight decline (Fig. S3 A). This indicates that WCS417 infection rapidly induces extensive translatome reprogramming in roots during the early colonization stage. As the treatment duration extended to 6 hours, the overall translational activity gradually returned toward the control level, suggesting a stabilization of the translational state. Notably, due to the relatively limited difference in TE between the 30-minute and 6-hour groups, no significantly enriched pathways were identified in the 6-hour versus 30-minute comparison. In contrast, functional pathway enrichment associated with TE changes was primarily observed at the 30 -minute post-inoculation time point. GO enrichment analysis of differentially translated genes showed that at 30 minutes post-inoculation, immune-related processes such as JA and SA signaling pathways were significantly upregulated at the TR level, consistent with translational and translational expression trends. This confirms that transient WCS417 infection rapidly triggers translational activation of immune pathways. By 6 hours, TR of the SA pathway remained elevated, further indicating that plants enhance the translation of immune components to balance symbiotic establishment with basal defense (Fig. 6 D, Table S7 ). Validation of changes in mRNA abundance during early WCS417 colonization by qRT-PCR To validate the reliability of our RNA-seq data, we selected key genes associated with immune response, root development, abiotic stress, and cold tolerance for qRT-PCR analysis. The results showed that the expression patterns of these genes were highly consistent with the transcriptome data (Fig. 7 , Fig. S4 ), confirming the accuracy and reproducibility of our sequencing results. This validation provides reliable experimental support for subsequent in-depth analyses based on the transcriptome data, thereby strengthening the credibility of the multi-omics integration findings in this study. To assess the translational changes induced by WCS417 in plant roots, we isolated ribosome-bound mRNAs using a sucrose cushion method and quantified the relative abundance of specific genes in this fraction by qPCR (Fig. 8 A-B). The results revealed significant differences in the level of target ribosome association genes across treatment time points, whereas the control gene ( ACTIN ) remained stable across groups (Fig. 8 B, Fig. S5 ). These findings demonstrate that WCS417 colonization triggers extensive translatome reprogramming in the roots of B. napus . Discussion Plant Growth-Promoting Rhizobacteria (PGPR) are well-known for their ability to enhance plant growth (Kloepper et al., 1980). The mechanisms underlying PGPR-mediated growth promotion have been extensively studied (Lugtenberg and Kamilova 2009 ; Verbon and Liberman 2016 ). Among them, P. simiae WCS417, a representative PGPR strain, efficiently colonizes plant roots and modulates rhizosphere development through multiple mechanisms to promote plant growth. (Zamioudis et al. 2013 ; Pieterse et al. 2020 ). Our study demonstrated that colonization of B. napus roots by WCS417 resulted in increased lateral root formation, reduced primary root length, and a significant increase in plant fresh weight (Fig. 1 ). We focused particularly on the transcriptional and translational regulatory mechanisms by which WCS417 influences root development in B. napus . Previous studies showed that WCS417 primarily modulates root architecture through auxin-dependent pathways, such as upregulating the expression of endogenous auxin biosynthesis genes (e.g., YUCCA family) and altering the localization and abundance of PIN proteins (e.g., PIN1, PIN2) to modify auxin distribution gradients, thereby promoting lateral root initiation and root hair formation (Zamioudis et al. 2013 ). Additionally, it activates Auxin Response Factors (ARFs) to drive the expression of downstream root development-related genes (Zamioudis et al. 2013 ). Consistently, we found that auxin-related genes such as YUC6 , WEI8 , and PIN3 showed significant upregulation at both transcriptional and translational levels at 6 hours post-WCS417 inoculation (Fig. 3 – 4 ). Moreover, WCS417 may regulate root architecture through cell wall remodeling and lignification (Marzorati et al. 2023 ). This study revealed that at 6 hours post-inoculation, cell wall-related genes (e.g., EXPA1 , EXPA10 , EXPA15 ) and root development-related genes (e.g., EP3 , SMB , CLE1 ) were significantly upregulated at the transcriptional and translational levels (Fig. 3 – 4 ). This suggests that WCS417 may facilitate structural reorganization by previously regulating genes associated with root morphogenesis. Meanwhile, we observed a significant downregulation in both the transcription and translation of the primary root elongation factor PXMT1 after six hours of infection, which may contribute to the observed inhibition of primary root growth (Fig. 1 , 3 ). The flagellin epitope (flg22₄₁₇) of WCS417 activates MAMP-triggered immunity (MTI) in plants (Gomez-Gomez et al. 1999 ; Millet et al. 2010 ; Pel and Pieterse 2013 ). However, the bacterium secretes gluconic acid and other metabolites to acidify the rhizosphere microenvironment, thereby suppressing immune responses, and simultaneously exhibits tolerance to antimicrobial coumarins produced via the MYB72 pathway (Yu et al. 2019a ; Yu et al. 2019b ; Stringlis et al. 2018 ). These synergistic mechanisms enable WCS417 to successfully colonize the host while evading immunity, ultimately establishing a stable mutualistic relationship (Gomez-Gomez et al. 1999 ; Pel and Pieterse 2013 ; Millet et al. 2010 ; Stringlis et al. 2018 ). Our findings reveal that immune pathways were upregulated at both transcriptional and translational levels at 30 minutes post-WCS417 inoculation, but were downregulated by 6 hours, a shift that may facilitate bacterial colonization (Fig. 3 – 5 ). Notably, however, the translation efficiency of genes associated with these immune pathways (e.g., CRK11 , HA5 , GR2 , ZRK10 ) was elevated at 30 minutes, and GO enrichment analysis still indicated upregulation of the SA immune pathway at 6 hours (Fig. 6 ). This suggests that although the plant attenuates immune-related gene expression to accommodate WCS417, it simultaneously enhances the translation efficiency of certain immune components to partially compensate for reduced transcript abundance, thereby maintaining basal defense capacity against potential pathogenic threats. In this study, we observed significant alterations in the expression of abiotic stress-related genes during colonization by WCS417. Specifically, positive regulators associated with drought and salt tolerance (e.g., ERF53 and ERF54 ) exhibited consistent upregulation at both transcriptional and translational levels, suggesting that WCS417 may enhance plant pre-adaptation to drought and salinity stress by activating these transcription factors (Fig. 3 ). In contrast, the expression of core regulators of the low-temperature response pathway (e.g., DREB1B , DREB1C , DREB1D , and DREB1E ) was persistently downregulated during the treatments (Fig. 3 ). This observation suggests that WCS417 may suppress the cold response pathway—or employ unexplored functions unrelated to cold tolerance but relevant to plant-microbe interactions—to reallocate plant resources, thereby prioritizing metabolic processes essential for establishing symbiosis. The functions of these transcription factors in plant-microbe interactions have not yet been systematically investigated. The observed downregulation of core cold-response factors during symbiosis establishment suggests that they may represent a novel regulatory node for balancing cold tolerance and mutualistic benefits in plants. Further elucidating the specific roles and regulatory mechanisms of these transcription factors within plant-microbe interaction networks will help reveal new strategies employed by plants to coordinate biotic and abiotic stress responses with microbial assistance and provide a theoretical basis for using beneficial microorganisms to improve crop stress tolerance. In summary, our findings demonstrate that during the early colonization of B. napus roots by WCS417, the host rapidly initiates transcriptional and translational reprogramming to respond to bacterial invasion, followed by gradual adjustments to stabilize the symbiotic association. This process involves multi-layered regulations, including auxin signaling, cell wall remodeling, immune balance, and abiotic stress, reflecting the complex and efficient molecular adaptation strategies employed in plant-PGPR interactions. However, the upstream regulators governing the immune-development balance—particularly those operating at the translational level, such as key receptors, protein kinases, transcription factors, and other core genes determining mRNA translation efficiency—remain unknown, and it is essential to investigate whether they function as central hubs that prioritize growth over defense. Future research should employ single-cell translatome sequencing technologies to elucidate the spatial architecture of gene expression and to decipher how WCS417 modulates post-transcriptional processes in specific cell layers, such as the root epidermis or cortex. Declarations Author Contribution L.Z. performed all the experiments, analyzed the data, and wrote the draft. J.L. analyzed the data. W.W. and Z.Z. conceived the experiments and wrote the manuscript. All authors have read and agreed to the published version of the manuscript. Acknowledgement We gratefully acknowledge Professor Yi Song from the Southern University of Science and Technology for providing the Pseudomonas simiae WCS417 strain. We also thank Dr. Shuchao Ren for his valuable support in bioinformatics analysis. The research was supported by Basic Research Project of Yazhouwan National Laboratory（2310YGL01）. References Aparicio MA, Ruiz-Castilla FJ, Ramos J, Romera FJ, Lucena C (2025) Pseudomonas simiae WCS417 Strain Enhances Tomato (Solanum lycopersicum L.) Plant Growth Under Alkaline Conditions. Plants (Basel) 14(2). 10.3390/plants14020264 Bizan J, Sarkar S, Basak AK, Bera S, Goto-Yamada S, Endo K, Tarnawska-Glatt K, Batth R, Bhardwaj K, Mirzaei M, Czerniawski P, Bednarek P, Yamada K (2025) Arabidopsis MYB47 and MYB95 transcription factors regulate jasmonate-inducible ER-body formation. Commun Biol 8(1):1377. 10.1038/s42003-025-08863-6 Bruckhoff V, Haroth S, Feussner K, Konig S, Brodhun F, Feussner I (2016) Functional Characterization of CYP94-Genes and Identification of a Novel Jasmonate Catabolite in Flowers. PLoS ONE 11(7):e0159875. 10.1371/journal.pone.0159875 Canchignia H, Altimira F, Montes C, Sanchez E, Tapia E, Miccono M, Espinoza D, Aguirre C, Seeger M, Prieto H (2017) Candidate nematicidal proteins in a new Pseudomonas veronii isolate identified by its antagonistic properties against Xiphinema index. J Gen Appl Microbiol 63(1):11–21. 10.2323/jgam.2016.07.001 Cha JY, Kim WY, Kang SB, Kim JI, Baek D, Jung IJ, Kim MR, Li N, Kim HJ, Nakajima M, Asami T, Sabir JS, Park HC, Lee SY, Bohnert HJ, Bressan RA, Pardo JM, Yun DJ (2015) A novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis. Nat Commun 6:8041. 10.1038/ncomms9041 Chandler JW, Werr W (2020) A phylogenetically conserved APETALA2/ETHYLENE RESPONSE FACTOR, ERF12, regulates Arabidopsis floral development. Plant Mol Biol 102(1–2):39–54. 10.1007/s11103-019-00936-5 Chen K, Du L, Chen Z (2003) Sensitization of defense responses and activation of programmed cell death by a pathogen-induced receptor-like protein kinase in Arabidopsis. Plant Mol Biol 53(1–2):61–74. 10.1023/B:PLAN.0000009265.72567.58 Chen S (2025) fastp 1.0: An ultra-fast all‐round tool for FASTQ data quality control and preprocessing. iMeta. 10.1002/imt2.70078 Chini A, Fonseca S, Fernandez G, Adie B, Chico JM, Lorenzo O, Garcia-Casado G, Lopez-Vidriero I, Lozano FM, Ponce MR, Micol JL, Solano R (2007) The JAZ family of repressors is the missing link in jasmonate signalling. Nature 448(7154):666–671. 10.1038/nature06006 Chung PJ, Park BS, Wang H, Liu J, Jang IC, Chua NH (2016) Light-Inducible MiR163 Targets PXMT1 Transcripts to Promote Seed Germination and Primary Root Elongation in Arabidopsis. Plant Physiol 170(3):1772–1782. 10.1104/pp.15.01188 Contreras-Cornejo HA, Macias-Rodriguez L, Cortes-Penagos C, Lopez-Bucio J (2009) Trichoderma virens, a plant beneficial fungus, enhances biomass production and promotes lateral root growth through an auxin-dependent mechanism in Arabidopsis. Plant Physiol 149(3):1579–1592. 10.1104/pp.108.130369 Cubero B, Nakagawa Y, Jiang XY, Miura KJ, Li F, Raghothama KG, Bressan RA, Hasegawa PM, Pardo JM (2009) The phosphate transporter PHT4;6 is a determinant of salt tolerance that is localized to the Golgi apparatus of Arabidopsis. Mol Plant 2(3):535–552. 10.1093/mp/ssp013 Desrut A, Moumen B, Thibault F, Le Hir R, Coutos-Thevenot P, Vriet C (2020) Beneficial rhizobacteria Pseudomonas simiae WCS417 induce major transcriptional changes in plant sugar transport. J Exp Bot 71(22):7301–7315. 10.1093/jxb/eraa396 Diplock N, Baudin M, Harden L, Silva CJ, Erickson-Beltran ML, Hassan JA, Lewis JD (2023) Utilising natural diversity of kinases to rationally engineer interactions with the angiosperm immune receptor ZAR1. Plant Cell Environ 46(7):2238–2254. 10.1111/pce.14603 Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21. 10.1093/bioinformatics/bts635 Du C, Bai H, Yan Y, Liu Y, Wang X, Zhang Z (2025) Exploring ABI5 regulation: Post-translational control and cofactor interactions in ABA signaling. Plant J 121(3):e17232. 10.1111/tpj.17232 Dyer SC, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Barrera-Enriquez VP, Becker A, Bennett R, Beracochea M, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Campbell LI, Martinez MC, Charkhchi M, Cortes LA, Davidson C, Denni S, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Falola O, Fatima R, Genez T, Martinez JG, Gurbich T, Hardy M, Hollis Z, Hunt T, Kay M, Kaykala V, Lemos D, Lodha D, Mathlouthi N, Merino GA, Merritt R, Mirabueno LP, Mushtaq A, Hossain SN, Perez-Silva JG, Perry M, Pilizota I, Poppleton D, Prosovetskaia I, Raj S, Salam AIA, Saraf S, Saraiva-Agostinho N, Sinha S, Sipos B, Sitnik V, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Tsang I, Urbina-Gomez D, Veidenberg A, Walsh TA, Willhoft NL, Allen J, Alvarez-Jarreta J, Chakiachvili M, Cheema J, da Rocha JB, De Silva NH, Giorgetti S, Haggerty L, Ilsley GR, Keatley J, Loveland JE, Moore B, Mudge JM, Naamati G, Tate J, Trevanion SJ, Winterbottom A, Flint B, Frankish A, Hunt SE, Finn RD, Freeberg MA, Harrison PW, Martin FJ, Yates AD (2025) Ensembl 2025. Nucleic Acids Res 53(D1):D948–D957. 10.1093/nar/gkae1071 Etchells JP, Moore L, Jiang WZ, Prescott H, Capper R, Saunders NJ, Bhatt AM, Dickinson HG (2012) A role for BELLRINGER in cell wall development is supported by loss-of-function phenotypes. BMC Plant Biol 12:212. 10.1186/1471-2229-12-212 Fang T, Hou J, He M, Wang L, Zheng M, Wang X, Xia J (2016) Actinidia chinensis Planch root extract (acRoots) inhibits hepatocellular carcinoma progression by inhibiting EP3 expression. Cell Biol Toxicol 32(6):499–511. 10.1007/s10565-016-9351-z Fowler SG, Cook D, Thomashow MF (2005) Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol 137(3):961–968. 10.1104/pp.104.058354 Froschel C, Komorek J, Attard A, Marsell A, Lopez-Arboleda WA, Le Berre J, Wolf E, Geldner N, Waller F, Korte A, Droge-Laser W (2021) Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes. Cell Host Microbe 29(2):299–310e297. 10.1016/j.chom.2020.11.014 Ge Y, Fang X, Liu W, Sheng L, Xu L (2019) Adventitious lateral rooting: the plasticity of root system architecture. Physiol Plant 165(1):39–43. 10.1111/ppl.12741 Gomez-Gomez L, Felix G, Boller T (1999) A single locus determines sensitivity to bacterial flagellin in Arabidopsis thaliana. Plant J 18(3):277–284. 10.1046/j.1365-313x.1999.00451.x Hacquard S, Spaepen S, Garrido-Oter R, Schulze-Lefert P (2017) Interplay Between Innate Immunity and the Plant Microbiota. Annu Rev Phytopathol 55:565–589. 10.1146/annurev-phyto-080516-035623 He R, Lv Z, Li Y, Ren S, Cao J, Zhu J, Zhang X, Wu H, Wan L, Tang J, Xu S, Chen X-L, Zhou Z (2024) tRNA-m1A methylation controls the infection of Magnaporthe oryzae by supporting ergosterol biosynthesis. Dev Cell 59(22):2931–2946e2937. 10.1016/j.devcel.2024.08.002 Hofmann E, Zerbe P, Schaller F (2006) The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction. Plant Cell 18(11):3201–3217. 10.1105/tpc.106.043984 Hou S, Tsuda K (2022) Salicylic acid and jasmonic acid crosstalk in plant immunity. Essays Biochem 66(5):647–656. 10.1042/EBC20210090 Huang PY, Catinot J, Zimmerli L (2016) Ethylene response factors in Arabidopsis immunity. J Exp Bot 67(5):1231–1241. 10.1093/jxb/erv518 Huang Y, Wang S, Wang C, Ding G, Cai H, Shi L, Xu F (2021) Induction of jasmonic acid biosynthetic genes inhibits Arabidopsis growth in response to low boron. J Integr Plant Biol 63(5):937–948. 10.1111/jipb.13048 Jacquot A, Chaput V, Mauries A, Li Z, Tillard P, Fizames C, Bonillo P, Bellegarde F, Laugier E, Santoni V, Hem S, Martin A, Gojon A, Schulze W, Lejay L (2020) NRT2.1 C-terminus phosphorylation prevents root high affinity nitrate uptake activity in Arabidopsis thaliana. New Phytol 228(3):1038–1054. 10.1111/nph.16710 Janda T, Szalai G, Pal M (2020) Salicylic Acid Signalling in Plants. Int J Mol Sci 21(7). 10.3390/ijms21072655 Kachroo P, Liu H, Kachroo A (2020) Salicylic acid: transport and long-distance immune signaling. Curr Opin Virol 42:53–57. 10.1016/j.coviro.2020.05.008 Koevoets IT, Venema JH, Elzenga JT, Testerink C (2016) Roots Withstanding their Environment: Exploiting Root System Architecture Responses to Abiotic Stress to Improve Crop Tolerance. Front Plant Sci 7:1335. 10.3389/fpls.2016.01335 Lange T, Atiq N, Pimenta Lange MJ (2023) GAS2 encodes a 2-oxoglutarate dependent dioxygenase involved in ABA catabolism. Nat Commun 14(1):7602. 10.1038/s41467-023-43187-1 Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. 10.1038/nmeth.1923 Li Q, Zhang X, Zhao P, Chen Y, Ni D, Wang M (2024) Metal tolerance protein CsMTP4 has dual functions in maintaining zinc homeostasis in tea plant. J Hazard Mater 471:134308. 10.1016/j.jhazmat.2024.134308 Liao Y, Smyth GK, Shi W (2013) The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 41(10):e108. 10.1093/nar/gkt214 Liu W, Sun J, Li J, Liu C, Si F, Yan B, Wang Z, Song X, Yang Y, Zhu Y, Cao X (2022) Reproductive tissue-specific translatome of a rice thermo-sensitive genic male sterile line. J Genet Genomics 49(7):624–635. 10.1016/j.jgg.2022.01.002 Long Y, Liu Z, Jia J, Mo W, Fang L, Lu D, Liu B, Zhang H, Chen W, Zhai J (2021) FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants. Genome Biol 22(1):66. 10.1186/s13059-021-02288-0 Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550. 10.1186/s13059-014-0550-8 Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556. 10.1146/annurev.micro.62.081307.162918 Leeman M, Van Pelt EMDOJA, Cornelissen C, Matamala-Garros A (1996) Schippers PAHMBaB Suppression of fusarium wilt of radish by co-inoculation of fluorescent Pseudomonas spp and root-colonizing fungi European Journal of Plant Pathology Mao P, Duan M, Wei C, Li Y (2007) WRKY62 transcription factor acts downstream of cytosolic NPR1 and negatively regulates jasmonate-responsive gene expression. Plant Cell Physiol 48(6):833–842. 10.1093/pcp/pcm058 Marzorati F, Rossi R, Bernardo L, Mauri P, Silvestre DD, Lauber E, Noel LD, Murgia I, Morandini P (2023) Arabidopsis thaliana Early Foliar Proteome Response to Root Exposure to the Rhizobacterium Pseudomonas simiae WCS417. Mol Plant Microbe Interact 36(11):737–748. 10.1094/MPMI-05-23-0071-R Merchante C, Hu Q, Heber S, Alonso J, Stepanova A (2016) A Ribosome Footprinting Protocol for Plants. Bio-Protocol 6(21). 10.21769/BioProtoc.1985 Miao P, Wang H, Wang W, Wang Z, Ke H, Cheng H, Ni J, Liang J, Yao YF, Wang J, Zhou JM, Lei X (2025) A widespread plant defense compound disarms bacterial type III injectisome assembly. Science 387(6737):eads0377. 10.1126/science.ads0377 Millet YA, Danna CH, Clay NK, Songnuan W, Simon MD, Werck-Reichhart D, Ausubel FM (2010) Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell 22(3):973–990. 10.1105/tpc.109.069658 Mlodzinska E, Zboinska M (2016) Phosphate Uptake and Allocation - A Closer Look at Arabidopsis thaliana L. and Oryza sativa L. Front Plant Sci 7:1198. 10.3389/fpls.2016.01198 Motte H, Vanneste S, Beeckman T (2019) Molecular and Environmental Regulation of Root Development. Annu Rev Plant Biol 70:465–488. 10.1146/annurev-arplant-050718-100423 Nakagami S, Aoyama T, Sato Y, Kajiwara T, Ishida T, Sawa S (2023) CLE3 and its homologs share overlapping functions in the modulation of lateral root formation through CLV1 and BAM1 in Arabidopsis thaliana. Plant J 113(6):1176–1191. 10.1111/tpj.16103 Nakano M, Kihara M, Iehata S, Tanaka R, Maeda H, Yoshikawa T (2011) Wax ester-like compounds as biosurfactants produced by Dietzia maris from n-alkane as a sole carbon source. J Basic Microbiol 51(5):490–498. 10.1002/jobm.201000420 Nel B, Steinberg C, Labuschagne N, Viljoen A (2006) The potential of nonpathogenic Fusarium oxysporum and other biological control organisms for suppressing fusarium wilt of banana. Plant Pathol 55(2):217–223. 10.1111/j.1365-3059.2006.01344.x Pel MJ, Pieterse CM (2013) Microbial recognition and evasion of host immunity. J Exp Bot 64(5):1237–1248. 10.1093/jxb/ers262 Perez-Alonso MM, Guerrero-Galan C, Gonzalez Ortega-Villaizan A, Ortiz-Garcia P, Scholz SS, Ramos P, Sakakibara H, Kiba T, Ludwig-Muller J, Krapp A, Oelmuller R, Vicente-Carbajosa J, Pollmann S (2022) The calcium sensor CBL7 is required for Serendipita indica-induced growth stimulation in Arabidopsis thaliana, controlling defense against the endophyte and K(+) homoeostasis in the symbiosis. Plant Cell Environ 45(11):3367–3382. 10.1111/pce.14420 Petricka JJ, Clay NK, Nelson TM (2008) Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana. Plant J 56(2):251–263. 10.1111/j.1365-313X.2008.03595.x Pieterse CMJ, Berendsen RL, de Jonge R, Stringlis IA, Van Dijken AJH, Van Pelt JA, Van Wees SCM, Yu K, Zamioudis C, Bakker PAHM (2020) Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium. Plant Soil 461(1–2):245–263. 10.1007/s11104-020-04786-9 Pratelli R, Voll LM, Horst RJ, Frommer WB, Pilot G (2010) Stimulation of nonselective amino acid export by glutamine dumper proteins. Plant Physiol 152(2):762–773. 10.1104/pp.109.151746 Ran LX, Liu CY, Wu GJ, van Loon LC, Bakker PAHM (2005) Suppression of bacterial wilt in Eucalyptus urophylla by fluorescent Pseudomonas spp. in China. Biol Control 32(1):111–120. 10.1016/j.biocontrol.2004.08.007 Ren S, Li Y, Zhou Z (2025) RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data. J Genet Genomics. 10.1016/j.jgg.2025.04.010 Ruan J, Zhou Y, Zhou M, Yan J, Khurshid M, Weng W, Cheng J, Zhang K (2019) Jasmonic Acid Signaling Pathway in Plants. Int J Mol Sci 20(10). 10.3390/ijms20102479 Schenk PM, Kazan K, Rusu AG, Manners JM, Maclean DJ (2005) The SEN1 gene of Arabidopsis is regulated by signals that link plant defence responses and senescence. Plant Physiol Biochem 43(10–11):997–1005. 10.1016/j.plaphy.2005.09.002 Shang E, Tu Q, Yu Z, Ding Z (2025) Cell wall dynamic changes and signaling during plant lateral root development. J Integr Plant Biol 67(3):632–648. 10.1111/jipb.13844 Shidore T, Triplett LR (2017) Toxin-Antitoxin Systems: Implications for Plant Disease. Annu Rev Phytopathol 55:161–179. 10.1146/annurev-phyto-080516-035559 Song J-M, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie W-Z, Cheng Y, Zhang Y, Liu K, Yang Q-Y, Chen L-L, Guo L (2020) Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants 6(1):34–45. 10.1038/s41477-019-0577-7 Stringlis IA, Proietti S, Hickman R, Van Verk MC, Zamioudis C, Pieterse CMJ (2018) Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists. Plant J 93(1):166–180. 10.1111/tpj.13741 Su YH, Frommer WB, Ludewig U (2004) Molecular and functional characterization of a family of amino acid transporters from Arabidopsis. Plant Physiol 136(2):3104–3113. 10.1104/pp.104.045278 Tao L, Wang L, Liu L, Cheng X, Zhang Q (2024) Phosphorous accumulation associated with mitochondrial PHT3-mediated enhanced arsenate tolerance in Chlamydomonas reinhardtii. J Hazard Mater 478:135460. 10.1016/j.jhazmat.2024.135460 Vacheron J, Desbrosses G, Renoud S, Padilla R, Walker V, Muller D, Prigent-Combaret C (2018) Differential Contribution of Plant-Beneficial Functions from Pseudomonas kilonensis F113 to Root System Architecture Alterations in Arabidopsis thaliana and Zea mays. Mol Plant Microbe Interact 31(2):212–223. 10.1094/MPMI-07-17-0185-R van Loon LC, Geraats BP, Linthorst HJ (2006) Ethylene as a modulator of disease resistance in plants. Trends Plant Sci 11(4):184–191. 10.1016/j.tplants.2006.02.005 Verbon EH, Liberman LM (2016) Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development. Trends Plant Sci 21(3):218–229. 10.1016/j.tplants.2016.01.013 Verbon EH, Trapet PL, Kruijs S, Temple-Boyer-Dury C, Rouwenhorst TG, Pieterse CMJ (2019) Rhizobacteria-Mediated Activation of the Fe Deficiency Response in Arabidopsis Roots: Impact on Fe Status and Signaling. Front Plant Sci 10:909. 10.3389/fpls.2019.00909 Verbon EH, Trapet PL, Stringlis IA, Kruijs S, Bakker P, Pieterse CMJ (2017) Iron and Immunity. Annu Rev Phytopathol 55:355–375. 10.1146/annurev-phyto-080516-035537 Vorwerk S, Schiff C, Santamaria M, Koh S, Nishimura M, Vogel J, Somerville C, Somerville S (2007) EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana. BMC Plant Biol 7:35. 10.1186/1471-2229-7-35 Vyse K, Schaarschmidt S, Erban A, Kopka J, Zuther E (2022) Specific CBF transcription factors and cold-responsive genes fine-tune the early triggering response after acquisition of cold priming and memory. Physiol Plant 174(4):e13740. 10.1111/ppl.13740 Wang T, Cui Y, Jin J, Guo J, Wang G, Yin X, He QY, Zhang G (2013) Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific. Nucleic Acids Res 41(9):4743–4754. 10.1093/nar/gkt178 Wang W, Bai XD, Chen K, Zhang XY, Gu CR, Jiang J, Yang CP, Liu GF (2022) PsnWRKY70 Negatively Regulates NaHCO(3) Tolerance in Populus. Int J Mol Sci 23(21). 10.3390/ijms232113086 Wang Z, Song Y (2022) Toward understanding the genetic bases underlying plant-mediated cry for help to the microbiota. Imeta 1(1):e8. 10.1002/imt2.8 Wu HL, Jen J, Hsu PY (2024) What, where, and how: Regulation of translation and the translational landscape in plants. Plant Cell 36(5):1540–1564. 10.1093/plcell/koad197 Yang Q, Li Z, Guan K, Wang Z, Tang X, Hong Y, Liu Z, Zhai J, Huang A, Long Y, Song Y (2025) Comparative single-nucleus RNA-seq analysis revealed localized and cell type-specific pathways governing root-microbiome interactions. Nat Commun 16(1):3169. 10.1038/s41467-025-58395-0 Yang TH, Lenglet-Hilfiker A, Stolz S, Glauser G, Farmer EE (2020) Jasmonate Precursor Biosynthetic Enzymes LOX3 and LOX4 Control Wound-Response Growth Restriction. Plant Physiol 184(2):1172–1180. 10.1104/pp.20.00471 Yang Z, Wang S, Wei L, Huang Y, Liu D, Jia Y, Luo C, Lin Y, Liang C, Hu Y, Dai C, Guo L, Zhou Y, Yang Q-Y (2023) BnIR: A multi-omics database with various tools for Brassica napus research and breeding. Mol Plant 16(4):775–789. 10.1016/j.molp.2023.03.007 Yu K, Liu Y, Tichelaar R, Savant N, Lagendijk E, van Kuijk SJL, Stringlis IA, van Dijken AJH, Pieterse CMJ, Bakker P, Haney CH, Berendsen RL (2019a) Rhizosphere-Associated Pseudomonas Suppress Local Root Immune Responses by Gluconic Acid-Mediated Lowering of Environmental pH. Curr Biol 29(22):3913–3920e3914. 10.1016/j.cub.2019.09.015 Yu K, Pieterse CMJ, Bakker P, Berendsen RL (2019b) Beneficial microbes going underground of root immunity. Plant Cell Environ 42(10):2860–2870. 10.1111/pce.13632 Yu Z, Qu X, Lv B, Li X, Sui J, Yu Q, Ding Z (2024) MAC3A and MAC3B mediate degradation of the transcription factor ERF13 and thus promote lateral root emergence. Plant Cell 36(9):3162–3176. 10.1093/plcell/koae047 Zamioudis C, Hanson J, Pieterse CM (2014) beta-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots. New Phytol 204(2):368–379. 10.1111/nph.12980 Zamioudis C, Korteland J, Van Pelt JA, van Hamersveld M, Dombrowski N, Bai Y, Hanson J, Van Verk MC, Ling HQ, Schulze-Lefert P, Pieterse CM (2015) Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses. Plant J 84(2):309–322. 10.1111/tpj.12995 Zamioudis C, Mastranesti P, Dhonukshe P, Blilou I, Pieterse CM (2013) Unraveling root developmental programs initiated by beneficial Pseudomonas spp. bacteria. Plant Physiol 162(1):304–318. 10.1104/pp.112.212597 Zarei A, Brikis CJ, Bajwa VS, Chiu GZ, Simpson JP, DeEll JR, Bozzo GG, Shelp BJ (2017) Plant Glyoxylate/Succinic Semialdehyde Reductases: Comparative Biochemical Properties, Function during Chilling Stress, and Subcellular Localization. Front Plant Sci 8:1399. 10.3389/fpls.2017.01399 Zhang J, Liu W, Bu J, Lin Y, Bai Y (2023) Host genetics regulate the plant microbiome. Curr Opin Microbiol 72:102268. 10.1016/j.mib.2023.102268 Zhao Z, Fan J, Gao YG, Wang Z, Yang P, Liang Y, Opiyo S, Xia Y (2022) Arabidopsis Plasma Membrane ATPase AHA5 Is Negatively Involved in PAMP-Triggered Immunity. Int J Mol Sci 23(7). 10.3390/ijms23073857 Zhong R, Lee C, Zhou J, McCarthy RL, Ye ZH (2008) A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20(10):2763–2782. 10.1105/tpc.108.061325 Zhou J, Uribe Acosta M, Stassen MJJ, Qi R, de Jonge R, White F, Kramer G, Dong L, Pieterse CMJ, Stringlis IA (2025) Arabidopsis root defense barriers support beneficial interactions with rhizobacterium Pseudomonas simiae WCS417. New Phytol. 10.1111/nph.70549 Additional Declarations No competing interests reported. Supplementary Files WCS417manuscriptsupplementalfigures.docx TableS1sequencingprofiles.xlsx TableS2RNAseqdifferentialexpreessiongenes.xlsx TableS3RNCseqdifferentialtranslationgenes.xlsx TableS4DEGSGOenrichment.xlsx TableS5DTGSGOenrichment.xlsx TableS6Differentialtranslationefficiencygenes.xlsx TableS7DTEGsGOenrichment.xlsx TableS8QuantitativePCRqPCRvalidationofdifferentiallyexpressedgenes.xlsx Cite Share Download PDF Status: Published Journal Publication published 12 Jan, 2026 Read the published version in Molecular Breeding → Version 1 posted Editorial decision: Revision requested 17 Nov, 2025 Reviews received at journal 15 Nov, 2025 Reviews received at journal 10 Nov, 2025 Reviewers agreed at journal 03 Nov, 2025 Reviewers agreed at journal 03 Nov, 2025 Reviewers invited by journal 03 Nov, 2025 Editor assigned by journal 03 Nov, 2025 Submission checks completed at journal 30 Oct, 2025 First submitted to journal 30 Oct, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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1","display":"","copyAsset":false,"role":"figure","size":215571,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eDevelopmental responses of\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eB. napus\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e seedlings to WCS417\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eA. \u003c/strong\u003eWCS417 induces changes in root architecture. \u003cstrong\u003eB-E.\u003c/strong\u003e Quantification of growth parameters in seedlings with or without WCS417 inoculation.\u003cstrong\u003e \u003c/strong\u003e(B)\u003cstrong\u003e \u003c/strong\u003eLateral root number. (C)\u003cstrong\u003e \u003c/strong\u003ePrimary root length. (D) Root fresh weight. (E) Shoot fresh weight. Significance analysis was calculated using GraphPad Prism 8 with an unpaired two-tailed Student's \u003cem\u003et\u003c/em\u003e-test. Error bars represent the standard deviation of six biological replicates. \u003cem\u003en\u003c/em\u003e = 6; Asterisks indicate significant differences between the two sets of data. \u003cem\u003e** P \u003c/em\u003e\u0026lt; 0.01，\u003cem\u003e*** P \u003c/em\u003e\u0026lt;0.001, \u003cem\u003e**** P \u003c/em\u003e\u0026lt; 0.0001. Scale bar, 1 cm.\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/ad8f996cf3c9f2a8b0fab36c.png"},{"id":95868066,"identity":"7176d6f1-67d1-4d1c-8a27-61ec5e20e7c2","added_by":"auto","created_at":"2025-11-13 19:58:31","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":60072,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePolysome profiling to detect global translation in \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eB. napus\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e roots before and upon WCS417 infection at 30 minutes and 6 hours.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eA.\u003c/strong\u003e Polysome profiling analysis. \u003cstrong\u003eB.\u003c/strong\u003eQuantification of the polysome-to-monosome (P/M) ratio. Significance analysis was calculated using GraphPad Prism 8 with an unpaired two-tailed Student's \u003cem\u003et\u003c/em\u003e-test. Error bars represent the standard deviation of three biological replicates. \u003cem\u003en\u003c/em\u003e= 3; Asterisks indicate significant differences between the two sets of data. \u003cem\u003e** P \u003c/em\u003e\u0026lt; 0.01，\u003cem\u003e*** P \u003c/em\u003e\u0026lt; 0.001, \u003cem\u003e**** P \u003c/em\u003e\u0026lt; 0.0001.\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/8bdc4cc06fef12333f1b60d6.png"},{"id":96240678,"identity":"19419fb0-604b-4179-9191-7ac7d6d9f35b","added_by":"auto","created_at":"2025-11-19 07:09:20","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":355244,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eVolcano plots display differentially expressed genes (DEGs) and differentially translated genes (DTGs) from RNA-seq and Ribo-seq data in \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eB. napus\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e roots under control versus WCS417 treatment at 30 minutes and 6 hours.\u003c/strong\u003e Genes related to immunity, stress response, and root development are highlighted with red circles. The dashed lines indicate the thresholds for significance (absolute fold change = 2, adjusted \u003cem\u003eP\u003c/em\u003e-value [Padj] = 0.05).\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/227dd6cc3110f74019534d19.png"},{"id":95868070,"identity":"916c14cd-8801-48b7-88c0-e8e773c3972a","added_by":"auto","created_at":"2025-11-13 19:58:32","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":204635,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGO functional annotation of differentially expressed genes in the transcriptome and translatome.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eA\u003c/strong\u003e. GO enrichment analysis of differentially expressed genes (DEGs) from the transcriptome. \u003cstrong\u003eB\u003c/strong\u003e. GO enrichment analysis of differentially translated genes (DTGs) from the translatome. The Y-axis represents the GO term names. The X-axis represents the different time-point comparisons of WCS417 treatment. The dot size corresponds to the number of genes enriched in the respective GO term, and the dot color intensity represents the -log₁₀ (adjusted \u003cem\u003eP\u003c/em\u003e-value). Adjusted \u003cem\u003eP\u003c/em\u003e-values were calculated using the clusterProfiler package with the Benjamini-Hochberg (BH) correction method.\u003c/p\u003e","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/7f545535e16c97f5ef4f07e5.png"},{"id":96241315,"identity":"4c9175a2-e920-448d-a376-b40c05b83e60","added_by":"auto","created_at":"2025-11-19 07:10:34","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":183081,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAnalysis of DEGs and DTEs from RNA-seq and RNC-seq data across different time points of WCS417 infection.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eA-B. \u003c/strong\u003eUpset plots showing the common and unique DEGs (upregulated or downregulated) across different time points in the RNA-seq (A) and RNC-seq (B) datasets. The top bar chart represents the number of upregulated (orange) or downregulated (blue) genes. The central vertical bars indicate the size of each specific intersection set; the height of each bar corresponds to the number of items (e.g., genes) in the intersection shown directly below it. The bottom matrix shows the composition of each intersection: each column represents an original set (time point comparison), filled dots represent items in each original set. All intersections are sorted by the number of items they contain, from largest to smallest. The green and dark red colors correspond to gene sets exhibiting specific transcriptional, translational, or coordinate functions that the set participates in the intersection above, and empty spaces indicate non-participation. The left-side bar chart displays the total number of transcriptional-translational activities at distinct time points. \u003cstrong\u003eC-E. \u003c/strong\u003eScatter plots showing the correlation between transcriptional and translational changes for genes. The grey horizontal and vertical lines represent the significance thresholds (±1 log2 fold change) for identifying genes with significant changes at the mRNA level (transcriptome) and the translation level (translatome), respectively.\u003c/p\u003e","description":"","filename":"floatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/69c976e0b9e82721367fa5f0.png"},{"id":95868078,"identity":"1920cea1-4808-42fd-809e-ddd2173da618","added_by":"auto","created_at":"2025-11-13 19:58:32","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":163982,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eAnalysis of differentially translated genes with altered translation Ratios (DTRGs) in \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eB. napus\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e roots under WCS417 treatment.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eA-C. \u003c/strong\u003eVolcano plots displaying DTEGs at different time points post-WCS417 treatment. The dashed lines indicate the thresholds for significance (fold change = 1.5, adjusted \u003cem\u003eP\u003c/em\u003e-value [Padj] = 0.05). \u003cstrong\u003eD.\u003c/strong\u003eGO enrichment analysis of DTEGs. The Y-axis represents the GO term names. The X-axis shows the different WCS417 treatment time-point comparisons. The dot size corresponds to the number of genes enriched in the respective GO term, and the dot color intensity represents the -log₁₀ (adjusted \u003cem\u003eP\u003c/em\u003e-value). Adjusted \u003cem\u003eP\u003c/em\u003e-values were calculated using the clusterProfiler package with the Benjamini-Hochberg (BH) correction method.\u003c/p\u003e","description":"","filename":"floatimage6.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/cf88d28baaea459bb02c3ba0.png"},{"id":96242018,"identity":"49ffa4c6-7f43-4469-befe-fa06a11d49db","added_by":"auto","created_at":"2025-11-19 07:11:52","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":66733,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eqRT-PCR analysis validates the expression patterns of key genes in response to WCS417 colonization.\u003c/strong\u003e Significance analysis was calculated using GraphPad Prism 8 with an unpaired two-tailed Student's \u003cem\u003et\u003c/em\u003e-test. Error bars represent the standard deviation of three biological replicates. \u003cem\u003en\u003c/em\u003e = 3; Asterisks indicate significant differences between the two sets of data. \u003cem\u003e* P \u003c/em\u003e\u0026lt; 0.05，\u003cem\u003e** P \u003c/em\u003e\u0026lt; 0.01，\u003cem\u003e*** P \u003c/em\u003e\u0026lt;0.001, \u003cem\u003e**** P \u003c/em\u003e\u0026lt; 0.0001.\u003c/p\u003e","description":"","filename":"floatimage7.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/5249e62971dda0281066d957.png"},{"id":96242733,"identity":"7005fb35-4709-4788-9cdc-1d04f70ec493","added_by":"auto","created_at":"2025-11-19 07:14:11","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":100243,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eRibosome occupancy of target mRNAs during WCS417 infection\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eA. \u003c/strong\u003eSucrose cushion schematic diagram. \u003cstrong\u003eB. \u003c/strong\u003eqPCR analysis to determine the percentage of mRNAs with altered translation rates (TR) in the sucrose cushion pellet fraction.\u003cstrong\u003e \u003c/strong\u003e\u003cem\u003eACTIN \u003c/em\u003eis the control. Significance analysis was calculated using GraphPad Prism 8 with an unpaired two-tailed Student's \u003cem\u003et\u003c/em\u003e-test. Asterisks indicate significant differences between the two\u003cstrong\u003e \u003c/strong\u003esets of data. Error bars represent the standard deviation of three biological replicates. \u003cem\u003en \u003c/em\u003e= 3; *, \u003cem\u003eP \u003c/em\u003e\u0026lt; 0.05; **, \u003cem\u003eP \u003c/em\u003e\u0026lt; 0.01.\u003c/p\u003e","description":"","filename":"floatimage8.png","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/46f9b76bf3f8179fa7cb30aa.png"},{"id":100614822,"identity":"cd81042d-d5ab-4c2a-8248-f6a1f5482928","added_by":"auto","created_at":"2026-01-19 17:26:08","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2269019,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/3e793ba4-a49b-45d0-8f71-82cd8219df63.pdf"},{"id":96240568,"identity":"5056975b-8e49-496a-a4f0-03a215bcd9d3","added_by":"auto","created_at":"2025-11-19 07:09:07","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":717305,"visible":true,"origin":"","legend":"","description":"","filename":"WCS417manuscriptsupplementalfigures.docx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/b7ac5d13a53c2e775ca7c2ec.docx"},{"id":96241378,"identity":"785f312f-f93e-4772-a8c1-8a9f7edf3775","added_by":"auto","created_at":"2025-11-19 07:10:39","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":9402,"visible":true,"origin":"","legend":"","description":"","filename":"TableS1sequencingprofiles.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/6e13a99d7350915f0969b98d.xlsx"},{"id":95868100,"identity":"ab43bc1b-5a5b-4dd5-841c-bbdcd0ddd24f","added_by":"auto","created_at":"2025-11-13 19:58:33","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":26694709,"visible":true,"origin":"","legend":"","description":"","filename":"TableS2RNAseqdifferentialexpreessiongenes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/9f6b1b971f0b1d77cb3ab709.xlsx"},{"id":95868099,"identity":"19b91497-452b-4b43-a7d2-b98c44bbc4d2","added_by":"auto","created_at":"2025-11-13 19:58:32","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":24439829,"visible":true,"origin":"","legend":"","description":"","filename":"TableS3RNCseqdifferentialtranslationgenes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/ad05adf54ede3584a9282ac2.xlsx"},{"id":95868072,"identity":"05b48c65-3acb-4a8c-a47e-58529f476916","added_by":"auto","created_at":"2025-11-13 19:58:32","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":21996,"visible":true,"origin":"","legend":"","description":"","filename":"TableS4DEGSGOenrichment.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/0c4d5aea6429b64eb690e5df.xlsx"},{"id":96241191,"identity":"8ac38848-7b4f-4872-a0e3-4083f6e050b2","added_by":"auto","created_at":"2025-11-19 07:10:21","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":20136,"visible":true,"origin":"","legend":"","description":"","filename":"TableS5DTGSGOenrichment.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/b81c9f83813127406dbec0f7.xlsx"},{"id":95868098,"identity":"22f07311-2d8e-42e8-83e4-e50fe59531c9","added_by":"auto","created_at":"2025-11-13 19:58:32","extension":"xlsx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":15823285,"visible":true,"origin":"","legend":"","description":"","filename":"TableS6Differentialtranslationefficiencygenes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/ce05cecf14d1712cb5856fef.xlsx"},{"id":96242097,"identity":"3f5bcd16-97d1-4e57-b108-a1afb5c0217c","added_by":"auto","created_at":"2025-11-19 07:12:00","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":21059,"visible":true,"origin":"","legend":"","description":"","filename":"TableS7DTEGsGOenrichment.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/a9a7374c965f563b9fb493bc.xlsx"},{"id":96242059,"identity":"28e198d2-56f3-4d93-993e-fdb45a8f7e5a","added_by":"auto","created_at":"2025-11-19 07:11:53","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":10564,"visible":true,"origin":"","legend":"","description":"","filename":"TableS8QuantitativePCRqPCRvalidationofdifferentiallyexpressedgenes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7990582/v1/9d44f4b6f47760fdf2d99582.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Integrated transcriptome and translatome analyses reveal the early regulatory network of Brassica napus roots in response to the growth-promoting rhizobacterium Pseudomonas simiae WCS417","fulltext":[{"header":"Introduction","content":"\u003cp\u003ePlants, as immobile organisms, have their roots constantly exposed to a highly complex soil microbial environment comprising diverse microbial communities, including beneficial, pathogenic, and commensal microorganisms (Yu et al. \u003cspan citationid=\"CR84\" class=\"CitationRef\"\u003e2019b\u003c/span\u003e). These microbial interactions have significant impacts on plant growth, development, immune responses, and environmental adaptation. To survive under such dynamic conditions, plants have evolved complex adaptive strategies, among which the selective recruitment of beneficial microbes stands out as a critical mechanism (Zhang et al. \u003cspan citationid=\"CR90\" class=\"CitationRef\"\u003e2023\u003c/span\u003e; Wang and Song \u003cspan citationid=\"CR78\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). This process involves the modulation of root morphology and physiological traits in response to microbial stimuli (Vacheron et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2018\u003c/span\u003e; Contreras-Cornejo et al. \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2009\u003c/span\u003e). Central to plant-microbe interactions is the recognition of microbe-associated molecular patterns (MAMPs), which trigger precise developmental reprogramming to facilitate symbiotic associations (Hacquard et al. \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Stringlis et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). Notably, these interactions induce dynamic remodeling of root architecture, characterized by the suppression of primary root elongation and the stimulation of lateral root proliferation. Such structural modifications ultimately enhance the plant\u0026rsquo;s capacity for resource acquisition, thereby optimizing water and nutrient uptake efficiency (Vacheron et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2018\u003c/span\u003e; Motte et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Koevoets et al. \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2016\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eSince its isolation from wheat roots in 1988, \u003cem\u003ePseudomonas simine\u003c/em\u003e WCS417 has been recognized as an important plant growth-promoting rhizobacterium (PGPR) (Pieterse et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). It effectively suppresses soil-borne diseases caused by fungi, bacteria, and nematodes, such as take-all and Fusarium wilt, while also enhancing tolerance to abiotic stresses, including drought and salinity (Nel et al. \u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e2006\u003c/span\u003e; Canchignia et al. \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; M. Leeman and Schippers 1996; Ran et al. \u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e2005\u003c/span\u003e). To date, it has been extensively studied and validated in more than 750 research studies (Pieterse et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2020\u003c/span\u003e), while the effect of WCS417 on B. napus has not been investigated to date.\u003c/p\u003e\u003cp\u003eWCS417 has been shown to markedly alter root system architecture, thereby improving water and nutrient uptake efficiency in many plant species (Aparicio et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2025\u003c/span\u003e; Zhou et al. \u003cspan citationid=\"CR93\" class=\"CitationRef\"\u003e2025\u003c/span\u003e; Stringlis et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). In model plants such as \u003cem\u003eArabidopsis thaliana\u003c/em\u003e, WCS417 colonization induces profound remodeling of root architecture, such as inhibition of primary root elongation, enhanced lateral root formation, and promotion of root hair development (Stringlis et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). These morphological alterations are orchestrated through complex interactions with auxin signaling pathways (Zamioudis et al. \u003cspan citationid=\"CR88\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Mechanistic studies reveal that WCS417 employs multiple synergistic strategies to influence plant growth. First, the bacterium synthesizes phytohormone, such as indole-3-acetic acid (IAA), which modulates the expression of auxin response factors (ARFs) to regulate the initiation and development of lateral root primordia (Zamioudis et al. \u003cspan citationid=\"CR88\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Second, volatile organic compounds (VOCs) produced by WCS417 induce the expression of root-specific transcription factor MYB72 to regulate root development (Zamioudis et al. \u003cspan citationid=\"CR87\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Zamioudis et al. \u003cspan citationid=\"CR86\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). Furthermore, both VOCs and microbial siderophores produced by WCS417 activate the MYB72-FIT1 signaling module, upregulating the expression of iron acquisition genes (\u003cem\u003eFRO2\u003c/em\u003e and \u003cem\u003eIRT1\u003c/em\u003e), thereby improving plant iron nutrition (Verbon et al. \u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Verbon et al. \u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). Additionally, WCS417 secretions specifically regulate the expression of sugar transporter proteins (SWEET11 and SWEET12), suggesting a sophisticated mechanism for optimizing carbon allocation during symbiotic interactions (Desrut et al. \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2020\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eIn plant roots, translational regulation serves as a critical mechanism of protein expression control that is not only involved in nutrient uptake, developmental processes, and adaptation to abiotic stress, but also plays a central role in root-microbe interactions (Li et al. \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2024\u003c/span\u003e; Yang et al. \u003cspan citationid=\"CR80\" class=\"CitationRef\"\u003e2025\u003c/span\u003e; Shang et al. \u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e2025\u003c/span\u003e; Du et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2025\u003c/span\u003e; Wu et al. \u003cspan citationid=\"CR79\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Recently developed protoplast-free single-nucleus RNA sequencing (snRNA-seq) has revealed that roots employ spatially partitioned and cell type-specific translational strategies to accurately distinguish beneficial from pathogenic microbes, maintain microbiome homeostasis, and coordinate immune responses. (Yang et al. \u003cspan citationid=\"CR80\" class=\"CitationRef\"\u003e2025\u003c/span\u003e; Long et al. \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). In the root meristematic zone, beneficial microbes significantly upregulate the expression of translation-related genes and promote the accumulation of ribosomal proteins and translation factors, thereby facilitating microbe-mediated growth promotion. In contrast, the mature zone employs localized translational mechanisms to activate immune responses, enabling rapid synthesis of defense-related proteins, including those involved in triterpenoid biosynthesis, to counteract pathogen invasion (Yang et al. \u003cspan citationid=\"CR80\" class=\"CitationRef\"\u003e2025\u003c/span\u003e). This spatially specialized translatability allows the root system to simultaneously promote beneficial symbiosis and effectively suppress harmful infections. Recent advances in cell type-specific ribosome profiling have further elucidated the spatial heterogeneity of translational dynamics in different root zones upon microbial contact, highlighting the key role of translational regulation in root-microbe interactions (Froschel et al. \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Liu et al. \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Thus, by precisely controlling the spatiotemporal production of proteins, translational regulation emerges as a core mechanism underlying root-microbial symbiosis, immune balance, and environmental adaptation.\u003c/p\u003e\u003cp\u003e\u003cem\u003eBrassica napus\u003c/em\u003e (\u003cem\u003eB. napus\u003c/em\u003e) is one of the most important oilseed crops worldwide. However, whether WCS417 could regulate root development and disease resistance in \u003cem\u003eB. napus\u003c/em\u003e remains largely uninvestigated. Furthermore, although translational regulation is critical for microbe-root interactions, systematic studies of the root translatome, particularly the molecular mechanisms underlying transient translational responses of plants during early colonization, remain relatively limited. In this study, we employed an integrated multi-omics approach, combining RNA-seq and RNC-seq (Ribosome Nascent-chain Complex sequencing) to systematically investigate the regulatory networks orchestrated by WCS417 at both transcriptional and translational levels during early colonization of \u003cem\u003eB. napus\u003c/em\u003e roots.\u003c/p\u003e"},{"header":"Method","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003ePlant material and growth conditions\u003c/h2\u003e\u003cp\u003e\u003cem\u003eBrassica napus\u003c/em\u003e seeds were surface sterilized with 75% ethanol for 8\u0026ndash;10 min, followed by 50% bleach for another 2 min, and then washed three times with sterilized water. Afterward, seeds were germinated on \u0026frac12; Murashige and Skoog (MS) agar plates with 0.5% sucrose in a growth chamber (22\u0026deg;C under a 16 h light/8 h dark period with light intensity at 450 \u0026micro;molm\u003csup\u003e\u0026minus;\u0026thinsp;2\u003c/sup\u003e s\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e) for 2 days.\u003c/p\u003e\u003cp\u003eFor measurement of plant biomass, Seedlings were transferred to \u0026frac12; MS agar plates or natural soil, and then plants were grown at 21\u0026deg;C growth room under a 16 h light/8 h dark period with light intensity at 450 \u0026micro;molm\u003csup\u003e\u0026minus;\u0026thinsp;2\u003c/sup\u003e s\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eFor the RNC-seq, seedlings were grown in liquid \u0026frac12; MS medium containing 2% (w/v) sucrose for 10 days (16 h Light/8 h Dark) and transferred to fresh liquid \u0026frac12; MS medium without sucrose for 2 more days before inoculation.\u003c/p\u003e\u003cp\u003e\u003cb\u003eCultivation of\u003c/b\u003e \u003cb\u003ePseudomonas simiae\u003c/b\u003e \u003cb\u003eWCS417 and treatment\u003c/b\u003e\u003c/p\u003e\u003cp\u003e\u003cem\u003ePseudomonas simiae\u003c/em\u003e WCS417 was cultured at 28\u0026deg;C on LB agar plates supplemented with 50 \u0026micro;g mL\u003csup\u003e\u0026minus;\u0026thinsp;1\u003c/sup\u003e of rifampicin. After 24 h of growth, cells were collected in 10 mM MgCl\u003csub\u003e2\u003c/sub\u003e, washed twice with 10 mM MgCl\u003csub\u003e2\u003c/sub\u003e by centrifugation for 5 min at 5000 g, and finally resuspended in ddH\u003csub\u003e2\u003c/sub\u003eO. For RNC-seq, WCS417 was diluted to OD600\u0026thinsp;=\u0026thinsp;0.5 in 10mM MgCl\u003csub\u003e2\u003c/sub\u003e and then added to the liquid rhizosphere to a final OD600 of 0.05. Liquid \u0026frac12; MS medium supplemented with an equal volume of 10mM MgCl\u003csub\u003e2\u003c/sub\u003e was used as a mock control.\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eMeasurement of plant biomass and parameters of root architecture\u003c/h3\u003e\n\u003cp\u003eFor treatment with live WCS417 cells, \u003cem\u003eBrassica napus\u003c/em\u003e seedlings were germinated on \u0026frac12; MS agar plates with 1% sucrose. two-day‐old \u003cem\u003eBrassica napus\u003c/em\u003e seedlings were transferred to new agar‐solidified \u0026frac12; MS plates with 1% sucrose with or without WCS417 (final concentration OD\u003csub\u003e600\u003c/sub\u003e\u0026thinsp;=\u0026thinsp;0.0005). Ten days after the start of the treatments, shoot fresh weight, primary root length, number of lateral roots, and hypocotyl length were determined.\u003c/p\u003e\n\u003ch3\u003eRibosome-nascent chain complex (RNC) extraction\u003c/h3\u003e\n\u003cp\u003eRNC extraction was performed as previously described (Wang et al. \u003cspan citationid=\"CR76\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). with minor modifications. Briefly, roots were ground using a pre-chilled mortar with the addition of 2 mL of cell lysis buffer (200 mM Tris\u0026ndash;HCl, pH 7.4, 35 mM MgCl₂, 200 mM KCl, 100 \u0026micro;g/mL cycloheximide, and 1% Triton X-100). After incubation on ice for 30 min, the lysates were centrifuged at 16,200 g for 20 min at 4\u0026deg;C. The supernatants were then layered onto 0.4 mL of a sucrose cushion buffer (1.75 M sucrose in gradient buffer). RNCs were pelleted by ultracentrifugation at 256,000 g for 3 h at 4\u0026deg;C (Merchante et al. \u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e2016\u003c/span\u003e).\u003c/p\u003e\n\u003ch3\u003eRNA-seq\u003c/h3\u003e\n\u003cp\u003eThe sequencing libraries were constructed following the Fast RNA-seq Lib Prep Kit V2 (ABclonal, #RK20306). Briefly, total RNA was isolated using TRNzol (TIANGEN, #DP424). Then, 1 \u0026micro;g of total RNA or RNC-mRNA was subjected to the polyA\u0026thinsp;+\u0026thinsp;mRNA isolation using the Poly(A) mRNA Capture Module beads (ABclonal, #RK20340) following the manufacturer\u0026rsquo;s instructions. The mRNA was fragmented at 94\u0026deg;C for 15 min to obtain 200\u0026ndash;250 bp inserts. First-strand cDNA was synthesized by First Strand Synthesis Enzyme Mix, and double-stranded cDNA was synthesized by Second Strand Master Mix using Second Strand \u0026amp; dA Buffer with dUTP *. The adapters were ligated by Ligase Mix T5. Ligated dscDNAs were purified and then amplified by 16 cycles of PCR with 2x PCR Master Mix and purified using AFTMag NGS DNA Clean Beads (ABclonal, #RK20257). Purified libraries were quantified by Qubit\u0026reg; 2.0 Fluorometer (Thermo Fisher, #Q33238). Libraries were barcoded, pooled, and sequenced in a HiSeq 2000 or 2500 machine (Paired-end 150-bp). High-quality reads that passed the Illumina quality filters were kept for the sequence analysis (Supplementary Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e).\u003c/p\u003e\u003cdiv id=\"Sec7\" class=\"Section2\"\u003e\u003ch2\u003eData analysis\u003c/h2\u003e\u003cp\u003eBoth RNA-Seq and RNC-Seq reads were first processed using fastp (v1.01) to remove adapter sequences (Chen \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2025\u003c/span\u003e). The resulting clean reads were then aligned to reference sequences of rRNA, tRNA, and other non-coding RNAs of \u003cem\u003eB. napus\u003c/em\u003e, obtained from the Ensembl database, using Bowtie2 (v2.5.4) (Dyer et al. \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e2025\u003c/span\u003e; Langmead and Salzberg \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e2012\u003c/span\u003e) to eliminate the contaminations. Subsequently, the filtered RNA-Seq and RNC-Seq reads were mapped to the B. napus reference genome (ZS11 v0), downloaded from the BnIR database, using STAR (v2.7.11b) (Song et al. \u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Yang et al. \u003cspan citationid=\"CR82\" class=\"CitationRef\"\u003e2023\u003c/span\u003e; Dobin et al. \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Gene expression quantification was performed using the featureCounts tool within the Subread package (v2.0.2) (Liao et al. \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e2013\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eQuality assessment of the processed datasets, including principal component analysis (PCA), enzymatic bias evaluation, gene coverage analysis, and sample reproducibility, was carried out using RiboShiny (v0.1), an integrated platform designed for comprehensive translation data analysis and visualization (Ren et al. \u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e2025\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eTo identify differentially expressed genes (DEGs), the DESeq2 package (v1.4) in R was applied using the likelihood ratio test, followed by shrinkage of log2 fold changes (LFC) via the lfcShrink function with the ashr estimator (Love et al. \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). Genes with an adjusted \u003cem\u003ep\u003c/em\u003e-value (Padj)\u0026thinsp;\u0026lt;\u0026thinsp;0.05 and |log₂(LFC)| \u0026ge; 0.585 were classified as differentially transcriptionally regulated. Translation ratios (TR) and differentially translated genes (DTRGs) were identified using the RiboShiny (v0.1) pipeline.\u003c/p\u003e\u003cp\u003eGene Ontology (GO) enrichment analysis for both DEGs and DTEGs was performed using the BnIR database, with a minimum count threshold of five genes per category.\u003c/p\u003e\u003c/div\u003e"},{"header":"Results","content":"\u003cp\u003e\u003cstrong\u003eDevelopmental responses of\u003c/strong\u003e \u003cstrong\u003eB. napus\u003c/strong\u003e \u003cstrong\u003eseedlings to WCS417\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIn this study, \u003cem\u003eB. napus\u003c/em\u003e cultivar Zhongshuang 11 (hereafter ZS11) was used to investigate the effects of WCS417 colonization on plant development. Two-day-old ZS11 seedlings were transferred to a \u0026frac12; MS plate with or without WCS417 suspension. After 10 days of incubation in the greenhouse, the growth of ZS11 seedlings with or without WCS417 treatment was examined. We found that there is a 3.18-fold increase in lateral root number and a 50.1\u0026thinsp;\u0026plusmn;\u0026thinsp;2.5% reduction in primary root length in the WCS417-treated seedlings compared with the control (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eA-C, Fig. \u003cspan class=\"InternalRef\"\u003eS1\u003c/span\u003e). In addition, WCS417 inoculation led to significant increases in both root (35.9\u0026thinsp;\u0026plusmn;\u0026thinsp;9.4%) and shoot (43.5\u0026thinsp;\u0026plusmn;\u0026thinsp;7.9%) fresh weight (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eD-E, Fig. \u003cspan class=\"InternalRef\"\u003eS1\u003c/span\u003e). These results align with earlier findings by Zamioudis et al. (\u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e) on WCS417-induced architectural remodeling in \u003cem\u003eArabidopsis thaliana\u003c/em\u003e, suggesting an evolutionary conservation of this PGPR\u0026rsquo;s growth-promoting property within the Brassicaceae family (Zamioudis et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e).\u003c/p\u003e\n\u003ch3\u003eWCS417 induces a transient boost in global translation in rapeseed roots during early colonization\u003c/h3\u003e\n\u003cp\u003eWCS417 colonization inhibits primary root growth, promotes lateral root development, and increases both roots and shoots biomass in \u003cem\u003eB. napus\u003c/em\u003e. These phenotypic changes align with prior observations in model plants, such as \u003cem\u003eArabidopsis thaliana\u003c/em\u003e (Zamioudis et al. \u003cspan class=\"CitationRef\"\u003e2013\u003c/span\u003e). Although the mechanisms regulating WCS417-mediated root development and growth have been extensively characterized in earlier studies, the translational regulatory mechanisms triggered by its colonization of host roots, particularly the transient translational responses during early colonization, remain poorly understood.\u003c/p\u003e\n\u003cp\u003eTo investigate the early translational response of rapeseed roots to \u003cem\u003ePseudomonas simiae\u003c/em\u003e WCS417, we performed polysome profiling at 30 minutes and 6 hours post-inoculation (He et al. \u003cspan class=\"CitationRef\"\u003e2024\u003c/span\u003e). The results demonstrated a significant increase in the polysome-to-monosome (P/M) ratio at both time points compared to the control, indicating a marked enhancement of global translational activity. Notably, the comparable P/M ratios between the 30-minute and 6-hour samples suggest that this heightened translational state is rapidly established and maintained during early colonization, rather than representing a fleeting response.\u003c/p\u003e\n\u003ch3\u003eRNA-seq and RNC-seq Quality Control Analysis\u003c/h3\u003e\n\u003cp\u003eTo investigate the role of translational regulation during early WCS417 colonization in root development, we performed an integrated analysis of transcriptome (RNA-seq) and translatome (RNC-seq) profiles. Two-day-old ZS11 seedlings were transplanted into liquid \u0026frac12; MS medium supplemented with 2% sucrose and grown in the greenhouse for 12 days. Seedlings were then treated with a bacterial suspension of WCS417 at OD₆₀₀ = 0.05 for either 30 minutes or 6 hours. Each biological replicate consisted of root tissues pooled from 5\u0026ndash;7 seedlings, with two independent replicates per condition.\u003c/p\u003e\n\u003cp\u003eThe collected samples were subjected to cell lysis, ribosome isolation, and extraction of ribosome-protected mRNA fragments. Subsequently, corresponding RNA-seq and RNC-seq libraries were constructed for each sample using commercial kits, followed by high-throughput sequencing for transcriptomic and translatomic analysis. Stringent quality control procedures were applied to the raw sequencing data. Each sample yielded more than 34\u0026nbsp;million raw reads, with Q30 scores exceeding 94%. No adapter contamination or abnormal GC content was detected based on assessments with FastQC and MultiQC. High-quality reads were aligned to the ZS11 reference genome using STAR, with a median unique mapping rate of 80%. Gene coverage uniformity was high without notable 3\u0026rsquo; bias, indicating high RNA integrity and library preparation quality. Collectively, these results confirm that the sequencing data are of high quality and suitable for subsequent analysis.\u003c/p\u003e\n\u003cp\u003eAfter verifying library quality, we further evaluated the reliability of the RNA-seq and RNC-seq data. Inter-sample correlation analysis showed that the correlation coefficients among biological replicates within each group (control, 30-minute, and 6-hour treatments) were close to 1, indicating high intra-group reproducibility, while clear differences were observed between groups (Fig. \u003cspan class=\"InternalRef\"\u003eS2\u003c/span\u003eC). Principal component analysis (PCA) further confirmed clear separation between control and treatment groups in the principal component space, demonstrating high reliability of the transcriptome data (Fig. \u003cspan class=\"InternalRef\"\u003eS2\u003c/span\u003eD). Pearson correlation heatmaps of RNA-seq and RNC-seq data across the three time points revealed substantial changes in gene expression patterns following WCS417 inoculation. PCA results indicated that transcriptional and translational alterations occurred as early as 30 minutes after inoculation, with more pronounced changes at 6 hours after inoculation (Fig. \u003cspan class=\"InternalRef\"\u003eS2\u003c/span\u003eD), suggesting that these responses are likely induced by WCS417 colonization.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eWCS417 modulates multiple physiological processes in\u003c/strong\u003e \u003cstrong\u003eB. napus\u003c/strong\u003e \u003cstrong\u003eroots during early colonization\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTo systematically investigate changes in gene expression, we performed differential expression analysis at both the transcriptome and translatome levels across all time points after normalization (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Table \u003cspan class=\"InternalRef\"\u003eS1\u003c/span\u003e). Scatter plots comprehensively display the distribution of differentially expressed genes (DGEs) and differentially translated genes (DTGs) for each comparison group, including WCS417 treatment for 30 minutes versus control, 6 hours versus control, and 6 hours versus 30 minutes. Transcriptome analysis revealed that compared to the control, WCS417 treatment for 30 minutes induced up-regulation of 1,806 genes and down-regulation of 1,117 genes; after 6 hours of treatment, the numbers of up- and down-regulated genes were 2,328 and 2,907, respectively; while the comparison between the 6-hour and 30-minute treatment groups identified 2106 up-regulated and 3100 down-regulated genes. At the translatome level, WCS417 treatment for 30 minutes versus control resulted in 1,762 up-regulated and 1,628 down-regulated genes; after 6 hours, 1,699 and 1,914 genes were up- and down-regulated, respectively; and the comparison between the two treatment time points showed 1,659 up-regulated and 2,645 down-regulated genes. Overall, WCS417 treatment induced extensive transcriptional and translational responses in the roots as early as 30 minutes, with the number of affected genes further increasing at 6 hours (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Table \u003cspan class=\"InternalRef\"\u003eS2\u003c/span\u003e-\u003cspan class=\"InternalRef\"\u003eS3\u003c/span\u003e).\u003c/p\u003e\n\u003cp\u003eIn the analysis of DEGs and DTGs, genes related to plant growth, development, and nutrient uptake were significantly affected. Genes associated with lateral root development (e.g., \u003cem\u003eCLE1\u003c/em\u003e and \u003cem\u003eWOX11\u003c/em\u003e) (Nakagami et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e; Ge et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e) were upregulated in response to WCS417 (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e), which is consistent with the phenotype that WCS417 promotes lateral root formation in \u003cem\u003eB. napus\u003c/em\u003e (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eA). On the other side, homologs of \u003cem\u003ePXMT1\u003c/em\u003e, which could promote primary root elongation (Chung et al. \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e), were firstly upregulated at 30 mins of WCS417 treatment, but significantly downregulated at both transcriptional and translational levels at 6 hours of WCS417 treatment (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e), which is in line with the long term suppression of primary root elongation by WCS417 (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eB).\u003c/p\u003e\n\u003cp\u003eConcurrently, notable changes were detected in genes related to nutrient absorption. The expression and translation of several homologs of \u003cem\u003eNRT2\u003c/em\u003e, a high-affinity nitrate transporter involved in nitrogen uptake (Jacquot et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e), were significantly upregulated 6 hours after inoculation. Meanwhile, the expression and translation of \u003cem\u003ePHT3\u003c/em\u003e homologs, which encode phosphate transporters (Mlodzinska and Zboinska \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e), also increased 6 hours after WCS417 inoculation. These results indicate that WCS417 colonization may enhance nitrogen and phosphate utilization and thereby promote plant growth (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eC, Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e\n\u003cp\u003eIn addition to growth and development-related genes, WCS417 treatment significantly affects the expression of many abiotic stress-related genes. Genes associated with antioxidant, drought, and salt stress responses (e.g., \u003cem\u003eERF53\u003c/em\u003e, \u003cem\u003eERF54\u003c/em\u003e, and \u003cem\u003eOXS3\u003c/em\u003e) exhibited elevated transcriptional and translational activity at both 30 minutes and 6 hours. The expression of \u003cem\u003eGAS2\u003c/em\u003e, an enzyme catabolizing ABA to phaseic acid (PA) and putative 8\u0026rsquo;-carboxy-ABA (Lange et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e), was consistently elevated at both time points. Interestingly, the expression of \u003cem\u003eDREB1B, DREB1C, DREB1D\u003c/em\u003e, and \u003cem\u003eDREB1E\u003c/em\u003e (Fowler et al. \u003cspan class=\"CitationRef\"\u003e2005\u003c/span\u003e; Vyse et al. \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e), core AP2/ERF family transcription factors in the low-temperature response pathway, was consistently reduced at both time points (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e). The function of these TFs in plant-microbe interaction was largely unexplored and worth further investigation.\u003c/p\u003e\n\u003cp\u003eWCS417 infection also dynamically modulated the expression of immune-related genes. For instance, positive immune regulators such as \u003cem\u003eSEN1\u003c/em\u003e (which acts downstream of the SA and JA signaling pathways) (Schenk et al. \u003cspan class=\"CitationRef\"\u003e2005\u003c/span\u003e) and \u003cem\u003eCBL7\u003c/em\u003e (a calcium sensor involved in immune signal transduction) (Perez-Alonso et al. \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e) were consistently up-regulated at both the transcriptional and translational levels at the two time points examined, indicating that transient WCS417 infection activates plant immune responses. In contrast, the expression of \u003cem\u003eCYP94B1\u003c/em\u003e, a negative regulator of JA signaling (Bruckhoff et al. \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e), was up-regulated at 30 minutes post-infection but down-regulated at 6 hours (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e). This expression pattern may help to alleviate the suppression of immune responses at later stages, thereby preventing excessive immune activation and facilitating a balance between growth and defense.\u003c/p\u003e\n\u003cp\u003eIn summary, these results demonstrate that during early colonization, WCS417 modulates multiple physiological processes, contributing to the rebalancing of plant immunity and development.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eWCS417 modulates immune responses in\u003c/strong\u003e \u003cstrong\u003eB. napus\u003c/strong\u003e \u003cstrong\u003eroots during early colonization\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTo further elucidate the regulatory patterns of gene expression during the symbiotic interaction between WCS417 and \u003cem\u003eB. napus\u003c/em\u003e roots, we performed Gene Ontology (GO) enrichment analysis on the differentially expressed genes (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e, Table\u003cspan class=\"InternalRef\"\u003eS4\u003c/span\u003e-\u003cspan class=\"InternalRef\"\u003eS5\u003c/span\u003e). The results indicated that both the transcriptomic and translatomic data were significantly enriched in pathways related to immune response, root development, hormone signaling, and amino acid transport during WCS417 infection, with the notable observation that several pathways enriched in the RNC-seq data (such as the jasmonic acid-mediated signaling pathway) were also detected in the RNA-seq data, suggesting a coordinated regulatory process from transcription to translation.\u003c/p\u003e\n\u003cp\u003ePrevious studies have indicated that although WCS417 is a non-pathogenic bacterium, its interaction with plant roots can still activate certain immune-related signaling pathways (Ruan et al. \u003cspan class=\"CitationRef\"\u003e2019\u003c/span\u003e; Hou and Tsuda \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e; Huang et al. \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e; van Loon et al. \u003cspan class=\"CitationRef\"\u003e2006\u003c/span\u003e; Janda et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e; Kachroo et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e; Miao et al. \u003cspan class=\"CitationRef\"\u003e2025\u003c/span\u003e; Shidore and Triplett \u003cspan class=\"CitationRef\"\u003e2017\u003c/span\u003e; Hacquard et al. \u003cspan class=\"CitationRef\"\u003e2017\u003c/span\u003e). Our results demonstrate that at the early stage of WCS417 inoculation (30 minutes), GO terms related to salicylic acid (SA), jasmonic acid (JA) signaling pathways were significantly upregulated (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003eA-B). As core components of the plant defense system, these pathways are known to comprehensively regulate immune responses (Mao et al. \u003cspan class=\"CitationRef\"\u003e2007\u003c/span\u003e; Hofmann et al. \u003cspan class=\"CitationRef\"\u003e2006\u003c/span\u003e; Vorwerk et al. \u003cspan class=\"CitationRef\"\u003e2007\u003c/span\u003e; Yang et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e). At the gene expression level, biosynthesis-related genes in the SA pathway (such as \u003cem\u003eWRKY28\u003c/em\u003e) and the JA pathway (such as \u003cem\u003eAOC2\u003c/em\u003e, \u003cem\u003eLOX3\u003c/em\u003e, and \u003cem\u003eLOX4\u003c/em\u003e) showed consistent upregulation at both transcriptional and translational levels (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e). These findings suggest that although WCS417 is a beneficial rhizobacterium, its initial colonization triggers an immune response in the plant, thereby inducing defense mechanisms to counteract WCS417 invasion.\u003c/p\u003e\n\u003cp\u003eIn the GO enrichment analysis conducted at 6 hours post-WCS417 infection and in comparison with the 30-minute time point, immune-related responses, including the JA and ET signaling pathways (e.g., \u003cem\u003eLOX3\u003c/em\u003e, \u003cem\u003eLOX4\u003c/em\u003e, \u003cem\u003ePDF1.4\u003c/em\u003e, \u003cem\u003eERF1A\u003c/em\u003e, \u003cem\u003eERF12\u003c/em\u003e, \u003cem\u003eERF13\u003c/em\u003e), exhibited a gradual downregulation trend (Chandler and Werr \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e; Yang et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e) (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e-\u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003eB). This shift suggests a potential transition of the plant from a defensive state toward symbiotic adaptation. Notably, at 30 minutes post-inoculation, the transcription factor \u003cem\u003eERF018\u003c/em\u003e, which regulates JA biosynthesis, was already significantly downregulated at both transcriptional and translational levels (Huang et al. \u003cspan class=\"CitationRef\"\u003e2021\u003c/span\u003e) (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e). This observation implies that JA biosynthesis-related genes may be initially modulated at the translational level to fine-tune the immune response, followed by subsequent transcriptional and translational regulation of JA synthesis-related genes by 6 hours post-infection.\u003c/p\u003e\n\u003cp\u003eConcurrently, genes associated with processes critical for symbiosis were upregulated at both transcriptional and translational levels. These included genes involved in cell wall remodeling (e.g., \u003cem\u003eEXPA1\u003c/em\u003e, \u003cem\u003eEXPA10\u003c/em\u003e, \u003cem\u003eEXPA15\u003c/em\u003e), root development (e.g., \u003cem\u003eEP3, SMB, CLE1\u003c/em\u003e), amino acid transport (e.g., \u003cem\u003eGDU6\u003c/em\u003e, \u003cem\u003eGDU1\u003c/em\u003e, \u003cem\u003eLHT1\u003c/em\u003e), and auxin biosynthesis (e.g., \u003cem\u003eYUC6, WEI8\u003c/em\u003e) (Cha et al. \u003cspan class=\"CitationRef\"\u003e2015\u003c/span\u003e; Fang et al. \u003cspan class=\"CitationRef\"\u003e2016\u003c/span\u003e; Jacquot et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e; Nakagami et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e; Nakano et al. \u003cspan class=\"CitationRef\"\u003e2011\u003c/span\u003e; Pratelli et al. \u003cspan class=\"CitationRef\"\u003e2010\u003c/span\u003e; Tao et al. \u003cspan class=\"CitationRef\"\u003e2024\u003c/span\u003e; Wang et al. \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e) (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e-\u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003eB). These changes suggest that the plant promotes root structural reorganization and hormonal responses to accommodate WCS417 colonization.\u003c/p\u003e\n\u003cp\u003eTo systematically investigate the coordinated and stage-specific regulation of transcription and translation across different time points, we employed UpSet plots to analyze gene sets that were either commonly or uniquely responsive at each time point (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003eA-B). The results revealed a substantial number of differentially expressed genes (DEGs) shared between the two time points at both transcriptional and translational levels. These common DEGs likely represent a persistent and core response essential for the interaction, potentially forming a \u0026ldquo;core response module\u0026rdquo; critical for the establishment of symbiosis. In addition, each treatment group contained genes that were specifically co-regulated at the transcriptional and translational levels in a time-dependent manner, as well as genes altered exclusively at either level. This pattern indicates that distinct physiological processes are regulated at different stages, highlighting the dynamic and phase-specific nature of the host response during WCS417 colonization.\u003c/p\u003e\n\u003cp\u003eFurthermore, the presence of independent transcriptional and translational DEG sets in the UpSet plot suggests that WCS417 treatment induces an imbalance between transcription and translation for a subset of root genes. To further dissect the coordination between transcriptional and translational regulation, we generated a nine-quadrant scatter plot based on transcript-level changes and translational-level changes (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003eC-E). Differential expression analysis was performed using DESeq2, and genes with an adjusted \u003cem\u003ep\u003c/em\u003e-value\u0026thinsp;\u0026gt;\u0026thinsp;0.05 were excluded.\u003c/p\u003e\n\u003cp\u003eThe results showed that during WCS417 colonization from 30 minutes to 6 hours, most genes exhibited consistent trends in both transcriptional and translational changes, indicating a coordinated regulatory mode (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003eC-E). However, a subset of genes displayed different changes, with misaligned mRNA expression and translation levels, some even showing opposite trends (e.g., upregulated mRNA with decreased translation, or downregulated mRNA accompanied by enhanced translation). These genes are likely subject to post-transcriptional regulation, suggesting that WCS417 infection specifically modulates the translation efficiency of certain genes.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eWCS417 fine-tunes the translational ratios of immune and root development genes\u003c/strong\u003e.\u003c/p\u003e\n\u003cp\u003eTo further elucidate the regulatory impact of WCS417 on translational control in \u003cem\u003eB\u003c/em\u003e. \u003cem\u003enapus\u003c/em\u003e roots, we compared translation ratios (TR) between untreated controls and roots treated for 30 minutes and 6 hours. After 30 minutes of WCS417 treatment, 3,223 genes exhibited significant changes in TR, with 3,021 exhibiting increased ratios and 202 showing decreased ratios, indicating that extensive translatome reprogramming had already occurred during the early inoculation stage, suggesting a critical role of translational regulation in the initial establishment of symbiosis (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003eA, Table \u003cspan class=\"InternalRef\"\u003eS6\u003c/span\u003e). After 6 hours of treatment, the number of genes with altered TR declined to 1,486, of which 1,006 showed elevated TR and 480 showed reduced TR, reflecting a more convergent translational response as the host adapted to bacterial colonization (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003eB, Table \u003cspan class=\"InternalRef\"\u003eS6\u003c/span\u003e). Notably, comparison with the 30-minute treatment group revealed TR alterations in 2,061 genes at the 6-hour time point, with 772 genes exhibiting increased TR and 1,289 showing decreased TR (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003eC, Table \u003cspan class=\"InternalRef\"\u003eS6\u003c/span\u003e). These genes are likely involved in maintaining cellular homeostasis or executing core regulatory functions during sustained symbiosis. Collectively, these results demonstrate that WCS417 infection triggers dynamic reprogramming of translation efficiency.\u003c/p\u003e\n\u003cp\u003eDifferential translation ratios (DTR) analysis revealed that WCS417 colonization triggers extensive translatome reprogramming during early infection. At 30 minutes post-inoculation, the TR of multiple immune-related genes (e.g., \u003cem\u003eCRK11\u003c/em\u003e, \u003cem\u003eHA5\u003c/em\u003e, \u003cem\u003eGR2\u003c/em\u003e, \u003cem\u003eZRK10\u003c/em\u003e, and \u003cem\u003eTIFY6B\u003c/em\u003e) was significantly elevated, indicating rapid activation of host immune responses upon initial contact (Chen et al. \u003cspan class=\"CitationRef\"\u003e2003\u003c/span\u003e; Zhao et al. \u003cspan class=\"CitationRef\"\u003e2022\u003c/span\u003e; Zarei et al. \u003cspan class=\"CitationRef\"\u003e2017\u003c/span\u003e; Diplock et al. \u003cspan class=\"CitationRef\"\u003e2023\u003c/span\u003e). Concurrently, increased TR of cell wall-related factors \u003cem\u003eMYB54\u003c/em\u003e and \u003cem\u003ePME5\u003c/em\u003e suggested that cell wall remodeling represents an early physiological adaptation to bacterial colonization (Zhong et al. \u003cspan class=\"CitationRef\"\u003e2008\u003c/span\u003e; Etchells et al. \u003cspan class=\"CitationRef\"\u003e2012\u003c/span\u003e) (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003eA).\u003c/p\u003e\n\u003cp\u003eAs colonization progressed to 6 hours, the TR of \u003cem\u003eERF13\u003c/em\u003e (Yu et al. \u003cspan class=\"CitationRef\"\u003e2024\u003c/span\u003e), a key transcription factor in the JA/ET signaling pathway, was consistently suppressed, while the immune negative regulator \u003cem\u003eHA5\u003c/em\u003e and \u003cem\u003eTIFY6B\u003c/em\u003e showed enhanced TR, implying that plants may selectively suppress certain immune pathways to facilitate symbiotic establishment (Chini et al. \u003cspan class=\"CitationRef\"\u003e2007\u003c/span\u003e). Furthermore, significantly increased TR of the endoplasmic reticulum formation-related gene \u003cem\u003eBGLU18\u003c/em\u003e and the amino acid transporter \u003cem\u003eCAT5\u003c/em\u003e at 6 hours suggested reinforced secretory capacity and nitrogen utilization to support host-microbe interface formation (Bizan et al. \u003cspan class=\"CitationRef\"\u003e2025\u003c/span\u003e; Su et al. \u003cspan class=\"CitationRef\"\u003e2004\u003c/span\u003e) (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003eB).\u003c/p\u003e\n\u003cp\u003eIn the 6-hour versus 30-minute comparison, sustained elevation in TR was observed for the phosphate transporter \u003cem\u003ePHT4\u003c/em\u003e (Cubero et al. \u003cspan class=\"CitationRef\"\u003e2009\u003c/span\u003e), root development-related gene \u003cem\u003eDOT4\u003c/em\u003e (Petricka et al. \u003cspan class=\"CitationRef\"\u003e2008\u003c/span\u003e), and the sucrose efflux transporter \u003cem\u003eSWEET15\u003c/em\u003e (Desrut et al. \u003cspan class=\"CitationRef\"\u003e2020\u003c/span\u003e), further supporting the role of WCS417 in enhancing nutrient acquisition and root development. Notably, tRNA methyltransferases \u003cem\u003eTRM8b\u003c/em\u003e and \u003cem\u003eTRM4B\u003c/em\u003e, which are critical for tRNA stability, proper folding, and overall translational accuracy, also exhibited significantly increased TR (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003eC). Their upregulation may systemically enhance global protein synthesis capacity during microbial colonization.\u003c/p\u003e\n\u003cp\u003eTo assess systematic differences in TR across treatment groups, we first visualized the overall TR distribution using empirical cumulative distribution function (ECDF) curves and boxplots (Fig. \u003cspan class=\"InternalRef\"\u003eS3\u003c/span\u003e). The results showed that compared to the control group, both the 30-minute and 6-hour treatment groups exhibited significantly higher overall TR levels, displaying a dynamic trend of initial increase followed by a slight decline (Fig. \u003cspan class=\"InternalRef\"\u003eS3\u003c/span\u003eA). This indicates that WCS417 infection rapidly induces extensive translatome reprogramming in roots during the early colonization stage. As the treatment duration extended to 6 hours, the overall translational activity gradually returned toward the control level, suggesting a stabilization of the translational state. Notably, due to the relatively limited difference in TE between the 30-minute and 6-hour groups, no significantly enriched pathways were identified in the 6-hour versus 30-minute comparison. In contrast, functional pathway enrichment associated with TE changes was primarily observed at the 30 -minute post-inoculation time point.\u003c/p\u003e\n\u003cp\u003eGO enrichment analysis of differentially translated genes showed that at 30 minutes post-inoculation, immune-related processes such as JA and SA signaling pathways were significantly upregulated at the TR level, consistent with translational and translational expression trends. This confirms that transient WCS417 infection rapidly triggers translational activation of immune pathways. By 6 hours, TR of the SA pathway remained elevated, further indicating that plants enhance the translation of immune components to balance symbiotic establishment with basal defense (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003eD, Table\u003cspan class=\"InternalRef\"\u003eS7\u003c/span\u003e).\u003c/p\u003e\n\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\n \u003ch2\u003eValidation of changes in mRNA abundance during early WCS417 colonization by qRT-PCR\u003c/h2\u003e\n \u003cp\u003eTo validate the reliability of our RNA-seq data, we selected key genes associated with immune response, root development, abiotic stress, and cold tolerance for qRT-PCR analysis. The results showed that the expression patterns of these genes were highly consistent with the transcriptome data (Fig. \u003cspan class=\"InternalRef\"\u003e7\u003c/span\u003e, Fig. \u003cspan class=\"InternalRef\"\u003eS4\u003c/span\u003e), confirming the accuracy and reproducibility of our sequencing results. This validation provides reliable experimental support for subsequent in-depth analyses based on the transcriptome data, thereby strengthening the credibility of the multi-omics integration findings in this study.\u003c/p\u003e\n \u003cp\u003eTo assess the translational changes induced by WCS417 in plant roots, we isolated ribosome-bound mRNAs using a sucrose cushion method and quantified the relative abundance of specific genes in this fraction by qPCR (Fig. \u003cspan class=\"InternalRef\"\u003e8\u003c/span\u003eA-B). The results revealed significant differences in the level of target ribosome association genes across treatment time points, whereas the control gene (\u003cem\u003eACTIN\u003c/em\u003e) remained stable across groups (Fig. \u003cspan class=\"InternalRef\"\u003e8\u003c/span\u003eB, Fig. \u003cspan class=\"InternalRef\"\u003eS5\u003c/span\u003e). These findings demonstrate that WCS417 colonization triggers extensive translatome reprogramming in the roots of \u003cem\u003eB. napus\u003c/em\u003e.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003ePlant Growth-Promoting Rhizobacteria (PGPR) are well-known for their ability to enhance plant growth (Kloepper et al., 1980). The mechanisms underlying PGPR-mediated growth promotion have been extensively studied (Lugtenberg and Kamilova \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e2009\u003c/span\u003e; Verbon and Liberman \u003cspan citationid=\"CR71\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Among them, \u003cem\u003eP. simiae\u003c/em\u003e WCS417, a representative PGPR strain, efficiently colonizes plant roots and modulates rhizosphere development through multiple mechanisms to promote plant growth. (Zamioudis et al. \u003cspan citationid=\"CR88\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Pieterse et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Our study demonstrated that colonization of \u003cem\u003eB. napus\u003c/em\u003e roots by WCS417 resulted in increased lateral root formation, reduced primary root length, and a significant increase in plant fresh weight (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eWe focused particularly on the transcriptional and translational regulatory mechanisms by which WCS417 influences root development in \u003cem\u003eB. napus\u003c/em\u003e. Previous studies showed that WCS417 primarily modulates root architecture through auxin-dependent pathways, such as upregulating the expression of endogenous auxin biosynthesis genes (e.g., \u003cem\u003eYUCCA\u003c/em\u003e family) and altering the localization and abundance of PIN proteins (e.g., PIN1, PIN2) to modify auxin distribution gradients, thereby promoting lateral root initiation and root hair formation (Zamioudis et al. \u003cspan citationid=\"CR88\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Additionally, it activates Auxin Response Factors (ARFs) to drive the expression of downstream root development-related genes (Zamioudis et al. \u003cspan citationid=\"CR88\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Consistently, we found that auxin-related genes such as \u003cem\u003eYUC6\u003c/em\u003e, \u003cem\u003eWEI8\u003c/em\u003e, and \u003cem\u003ePIN3\u003c/em\u003e showed significant upregulation at both transcriptional and translational levels at 6 hours post-WCS417 inoculation (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eMoreover, WCS417 may regulate root architecture through cell wall remodeling and lignification (Marzorati et al. \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). This study revealed that at 6 hours post-inoculation, cell wall-related genes (e.g., \u003cem\u003eEXPA1\u003c/em\u003e, \u003cem\u003eEXPA10\u003c/em\u003e, \u003cem\u003eEXPA15\u003c/em\u003e) and root development-related genes (e.g., \u003cem\u003eEP3\u003c/em\u003e, \u003cem\u003eSMB\u003c/em\u003e, \u003cem\u003eCLE1\u003c/em\u003e) were significantly upregulated at the transcriptional and translational levels (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). This suggests that WCS417 may facilitate structural reorganization by previously regulating genes associated with root morphogenesis. Meanwhile, we observed a significant downregulation in both the transcription and translation of the primary root elongation factor \u003cem\u003ePXMT1\u003c/em\u003e after six hours of infection, which may contribute to the observed inhibition of primary root growth (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, \u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eThe flagellin epitope (flg22₄₁₇) of WCS417 activates MAMP-triggered immunity (MTI) in plants (Gomez-Gomez et al. \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e1999\u003c/span\u003e; Millet et al. \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2010\u003c/span\u003e; Pel and Pieterse \u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). However, the bacterium secretes gluconic acid and other metabolites to acidify the rhizosphere microenvironment, thereby suppressing immune responses, and simultaneously exhibits tolerance to antimicrobial coumarins produced via the MYB72 pathway (Yu et al. \u003cspan citationid=\"CR83\" class=\"CitationRef\"\u003e2019a\u003c/span\u003e; Yu et al. \u003cspan citationid=\"CR84\" class=\"CitationRef\"\u003e2019b\u003c/span\u003e; Stringlis et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). These synergistic mechanisms enable WCS417 to successfully colonize the host while evading immunity, ultimately establishing a stable mutualistic relationship (Gomez-Gomez et al. \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e1999\u003c/span\u003e; Pel and Pieterse \u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Millet et al. \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2010\u003c/span\u003e; Stringlis et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). Our findings reveal that immune pathways were upregulated at both transcriptional and translational levels at 30 minutes post-WCS417 inoculation, but were downregulated by 6 hours, a shift that may facilitate bacterial colonization (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e). Notably, however, the translation efficiency of genes associated with these immune pathways (e.g., \u003cem\u003eCRK11\u003c/em\u003e, \u003cem\u003eHA5\u003c/em\u003e, \u003cem\u003eGR2\u003c/em\u003e, \u003cem\u003eZRK10\u003c/em\u003e) was elevated at 30 minutes, and GO enrichment analysis still indicated upregulation of the SA immune pathway at 6 hours (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). This suggests that although the plant attenuates immune-related gene expression to accommodate WCS417, it simultaneously enhances the translation efficiency of certain immune components to partially compensate for reduced transcript abundance, thereby maintaining basal defense capacity against potential pathogenic threats.\u003c/p\u003e\u003cp\u003eIn this study, we observed significant alterations in the expression of abiotic stress-related genes during colonization by WCS417. Specifically, positive regulators associated with drought and salt tolerance (e.g., \u003cem\u003eERF53\u003c/em\u003e and \u003cem\u003eERF54\u003c/em\u003e) exhibited consistent upregulation at both transcriptional and translational levels, suggesting that WCS417 may enhance plant pre-adaptation to drought and salinity stress by activating these transcription factors (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). In contrast, the expression of core regulators of the low-temperature response pathway (e.g., \u003cem\u003eDREB1B\u003c/em\u003e, \u003cem\u003eDREB1C\u003c/em\u003e, \u003cem\u003eDREB1D\u003c/em\u003e, and \u003cem\u003eDREB1E\u003c/em\u003e) was persistently downregulated during the treatments (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). This observation suggests that WCS417 may suppress the cold response pathway\u0026mdash;or employ unexplored functions unrelated to cold tolerance but relevant to plant-microbe interactions\u0026mdash;to reallocate plant resources, thereby prioritizing metabolic processes essential for establishing symbiosis.\u003c/p\u003e\u003cp\u003eThe functions of these transcription factors in plant-microbe interactions have not yet been systematically investigated. The observed downregulation of core cold-response factors during symbiosis establishment suggests that they may represent a novel regulatory node for balancing cold tolerance and mutualistic benefits in plants. Further elucidating the specific roles and regulatory mechanisms of these transcription factors within plant-microbe interaction networks will help reveal new strategies employed by plants to coordinate biotic and abiotic stress responses with microbial assistance and provide a theoretical basis for using beneficial microorganisms to improve crop stress tolerance.\u003c/p\u003e\u003cp\u003eIn summary, our findings demonstrate that during the early colonization of \u003cem\u003eB. napus\u003c/em\u003e roots by WCS417, the host rapidly initiates transcriptional and translational reprogramming to respond to bacterial invasion, followed by gradual adjustments to stabilize the symbiotic association. This process involves multi-layered regulations, including auxin signaling, cell wall remodeling, immune balance, and abiotic stress, reflecting the complex and efficient molecular adaptation strategies employed in plant-PGPR interactions. However, the upstream regulators governing the immune-development balance\u0026mdash;particularly those operating at the translational level, such as key receptors, protein kinases, transcription factors, and other core genes determining mRNA translation efficiency\u0026mdash;remain unknown, and it is essential to investigate whether they function as central hubs that prioritize growth over defense. Future research should employ single-cell translatome sequencing technologies to elucidate the spatial architecture of gene expression and to decipher how WCS417 modulates post-transcriptional processes in specific cell layers, such as the root epidermis or cortex.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eL.Z. performed all the experiments, analyzed the data, and wrote the draft. J.L. analyzed the data. W.W. and Z.Z. conceived the experiments and wrote the manuscript. All authors have read and agreed to the published version of the manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eWe gratefully acknowledge Professor Yi Song from the Southern University of Science and Technology for providing the Pseudomonas simiae WCS417 strain. We also thank Dr. Shuchao Ren for his valuable support in bioinformatics analysis. The research was supported by Basic Research Project of Yazhouwan National Laboratory（2310YGL01）.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eAparicio MA, Ruiz-Castilla FJ, Ramos J, Romera FJ, Lucena C (2025) Pseudomonas simiae WCS417 Strain Enhances Tomato (Solanum lycopersicum L.) Plant Growth Under Alkaline Conditions. Plants (Basel) 14(2). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/plants14020264\u003c/span\u003e\u003cspan address=\"10.3390/plants14020264\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eBizan J, Sarkar S, Basak AK, Bera S, Goto-Yamada S, Endo K, Tarnawska-Glatt K, Batth R, Bhardwaj K, Mirzaei M, Czerniawski P, Bednarek P, Yamada K (2025) Arabidopsis MYB47 and MYB95 transcription factors regulate jasmonate-inducible ER-body formation. Commun Biol 8(1):1377. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s42003-025-08863-6\u003c/span\u003e\u003cspan address=\"10.1038/s42003-025-08863-6\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eBruckhoff V, Haroth S, Feussner K, Konig S, Brodhun F, Feussner I (2016) Functional Characterization of CYP94-Genes and Identification of a Novel Jasmonate Catabolite in Flowers. PLoS ONE 11(7):e0159875. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1371/journal.pone.0159875\u003c/span\u003e\u003cspan address=\"10.1371/journal.pone.0159875\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eCanchignia H, Altimira F, Montes C, Sanchez E, Tapia E, Miccono M, Espinoza D, Aguirre C, Seeger M, Prieto H (2017) Candidate nematicidal proteins in a new Pseudomonas veronii isolate identified by its antagonistic properties against Xiphinema index. J Gen Appl Microbiol 63(1):11\u0026ndash;21. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.2323/jgam.2016.07.001\u003c/span\u003e\u003cspan address=\"10.2323/jgam.2016.07.001\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eCha JY, Kim WY, Kang SB, Kim JI, Baek D, Jung IJ, Kim MR, Li N, Kim HJ, Nakajima M, Asami T, Sabir JS, Park HC, Lee SY, Bohnert HJ, Bressan RA, Pardo JM, Yun DJ (2015) A novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis. Nat Commun 6:8041. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/ncomms9041\u003c/span\u003e\u003cspan address=\"10.1038/ncomms9041\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChandler JW, Werr W (2020) A phylogenetically conserved APETALA2/ETHYLENE RESPONSE FACTOR, ERF12, regulates Arabidopsis floral development. Plant Mol Biol 102(1\u0026ndash;2):39\u0026ndash;54. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1007/s11103-019-00936-5\u003c/span\u003e\u003cspan address=\"10.1007/s11103-019-00936-5\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChen K, Du L, Chen Z (2003) Sensitization of defense responses and activation of programmed cell death by a pathogen-induced receptor-like protein kinase in Arabidopsis. Plant Mol Biol 53(1\u0026ndash;2):61\u0026ndash;74. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1023/B:PLAN.0000009265.72567.58\u003c/span\u003e\u003cspan address=\"10.1023/B:PLAN.0000009265.72567.58\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChen S (2025) fastp 1.0: An ultra-fast all‐round tool for FASTQ data quality control and preprocessing. iMeta. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1002/imt2.70078\u003c/span\u003e\u003cspan address=\"10.1002/imt2.70078\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChini A, Fonseca S, Fernandez G, Adie B, Chico JM, Lorenzo O, Garcia-Casado G, Lopez-Vidriero I, Lozano FM, Ponce MR, Micol JL, Solano R (2007) The JAZ family of repressors is the missing link in jasmonate signalling. Nature 448(7154):666\u0026ndash;671. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/nature06006\u003c/span\u003e\u003cspan address=\"10.1038/nature06006\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChung PJ, Park BS, Wang H, Liu J, Jang IC, Chua NH (2016) Light-Inducible MiR163 Targets PXMT1 Transcripts to Promote Seed Germination and Primary Root Elongation in Arabidopsis. Plant Physiol 170(3):1772\u0026ndash;1782. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1104/pp.15.01188\u003c/span\u003e\u003cspan address=\"10.1104/pp.15.01188\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eContreras-Cornejo HA, Macias-Rodriguez L, Cortes-Penagos C, Lopez-Bucio J (2009) Trichoderma virens, a plant beneficial fungus, enhances biomass production and promotes lateral root growth through an auxin-dependent mechanism in Arabidopsis. Plant Physiol 149(3):1579\u0026ndash;1592. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1104/pp.108.130369\u003c/span\u003e\u003cspan address=\"10.1104/pp.108.130369\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eCubero B, Nakagawa Y, Jiang XY, Miura KJ, Li F, Raghothama KG, Bressan RA, Hasegawa PM, Pardo JM (2009) The phosphate transporter PHT4;6 is a determinant of salt tolerance that is localized to the Golgi apparatus of Arabidopsis. Mol Plant 2(3):535\u0026ndash;552. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/mp/ssp013\u003c/span\u003e\u003cspan address=\"10.1093/mp/ssp013\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDesrut A, Moumen B, Thibault F, Le Hir R, Coutos-Thevenot P, Vriet C (2020) Beneficial rhizobacteria Pseudomonas simiae WCS417 induce major transcriptional changes in plant sugar transport. J Exp Bot 71(22):7301\u0026ndash;7315. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/jxb/eraa396\u003c/span\u003e\u003cspan address=\"10.1093/jxb/eraa396\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDiplock N, Baudin M, Harden L, Silva CJ, Erickson-Beltran ML, Hassan JA, Lewis JD (2023) Utilising natural diversity of kinases to rationally engineer interactions with the angiosperm immune receptor ZAR1. Plant Cell Environ 46(7):2238\u0026ndash;2254. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/pce.14603\u003c/span\u003e\u003cspan address=\"10.1111/pce.14603\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15\u0026ndash;21. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/bioinformatics/bts635\u003c/span\u003e\u003cspan address=\"10.1093/bioinformatics/bts635\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDu C, Bai H, Yan Y, Liu Y, Wang X, Zhang Z (2025) Exploring ABI5 regulation: Post-translational control and cofactor interactions in ABA signaling. Plant J 121(3):e17232. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/tpj.17232\u003c/span\u003e\u003cspan address=\"10.1111/tpj.17232\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDyer SC, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Barrera-Enriquez VP, Becker A, Bennett R, Beracochea M, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Campbell LI, Martinez MC, Charkhchi M, Cortes LA, Davidson C, Denni S, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Falola O, Fatima R, Genez T, Martinez JG, Gurbich T, Hardy M, Hollis Z, Hunt T, Kay M, Kaykala V, Lemos D, Lodha D, Mathlouthi N, Merino GA, Merritt R, Mirabueno LP, Mushtaq A, Hossain SN, Perez-Silva JG, Perry M, Pilizota I, Poppleton D, Prosovetskaia I, Raj S, Salam AIA, Saraf S, Saraiva-Agostinho N, Sinha S, Sipos B, Sitnik V, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Tsang I, Urbina-Gomez D, Veidenberg A, Walsh TA, Willhoft NL, Allen J, Alvarez-Jarreta J, Chakiachvili M, Cheema J, da Rocha JB, De Silva NH, Giorgetti S, Haggerty L, Ilsley GR, Keatley J, Loveland JE, Moore B, Mudge JM, Naamati G, Tate J, Trevanion SJ, Winterbottom A, Flint B, Frankish A, Hunt SE, Finn RD, Freeberg MA, Harrison PW, Martin FJ, Yates AD (2025) Ensembl 2025. Nucleic Acids Res 53(D1):D948\u0026ndash;D957. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/nar/gkae1071\u003c/span\u003e\u003cspan address=\"10.1093/nar/gkae1071\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eEtchells JP, Moore L, Jiang WZ, Prescott H, Capper R, Saunders NJ, Bhatt AM, Dickinson HG (2012) A role for BELLRINGER in cell wall development is supported by loss-of-function phenotypes. BMC Plant Biol 12:212. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1186/1471-2229-12-212\u003c/span\u003e\u003cspan address=\"10.1186/1471-2229-12-212\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eFang T, Hou J, He M, Wang L, Zheng M, Wang X, Xia J (2016) Actinidia chinensis Planch root extract (acRoots) inhibits hepatocellular carcinoma progression by inhibiting EP3 expression. Cell Biol Toxicol 32(6):499\u0026ndash;511. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1007/s10565-016-9351-z\u003c/span\u003e\u003cspan address=\"10.1007/s10565-016-9351-z\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eFowler SG, Cook D, Thomashow MF (2005) Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol 137(3):961\u0026ndash;968. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1104/pp.104.058354\u003c/span\u003e\u003cspan address=\"10.1104/pp.104.058354\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eFroschel C, Komorek J, Attard A, Marsell A, Lopez-Arboleda WA, Le Berre J, Wolf E, Geldner N, Waller F, Korte A, Droge-Laser W (2021) Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes. Cell Host Microbe 29(2):299\u0026ndash;310e297. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.chom.2020.11.014\u003c/span\u003e\u003cspan address=\"10.1016/j.chom.2020.11.014\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eGe Y, Fang X, Liu W, Sheng L, Xu L (2019) Adventitious lateral rooting: the plasticity of root system architecture. Physiol Plant 165(1):39\u0026ndash;43. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/ppl.12741\u003c/span\u003e\u003cspan address=\"10.1111/ppl.12741\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eGomez-Gomez L, Felix G, Boller T (1999) A single locus determines sensitivity to bacterial flagellin in Arabidopsis thaliana. Plant J 18(3):277\u0026ndash;284. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1046/j.1365-313x.1999.00451.x\u003c/span\u003e\u003cspan address=\"10.1046/j.1365-313x.1999.00451.x\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHacquard S, Spaepen S, Garrido-Oter R, Schulze-Lefert P (2017) Interplay Between Innate Immunity and the Plant Microbiota. Annu Rev Phytopathol 55:565\u0026ndash;589. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1146/annurev-phyto-080516-035623\u003c/span\u003e\u003cspan address=\"10.1146/annurev-phyto-080516-035623\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHe R, Lv Z, Li Y, Ren S, Cao J, Zhu J, Zhang X, Wu H, Wan L, Tang J, Xu S, Chen X-L, Zhou Z (2024) tRNA-m1A methylation controls the infection of Magnaporthe oryzae by supporting ergosterol biosynthesis. Dev Cell 59(22):2931\u0026ndash;2946e2937. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.devcel.2024.08.002\u003c/span\u003e\u003cspan address=\"10.1016/j.devcel.2024.08.002\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHofmann E, Zerbe P, Schaller F (2006) The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction. Plant Cell 18(11):3201\u0026ndash;3217. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1105/tpc.106.043984\u003c/span\u003e\u003cspan address=\"10.1105/tpc.106.043984\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHou S, Tsuda K (2022) Salicylic acid and jasmonic acid crosstalk in plant immunity. Essays Biochem 66(5):647\u0026ndash;656. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1042/EBC20210090\u003c/span\u003e\u003cspan address=\"10.1042/EBC20210090\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHuang PY, Catinot J, Zimmerli L (2016) Ethylene response factors in Arabidopsis immunity. J Exp Bot 67(5):1231\u0026ndash;1241. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/jxb/erv518\u003c/span\u003e\u003cspan address=\"10.1093/jxb/erv518\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHuang Y, Wang S, Wang C, Ding G, Cai H, Shi L, Xu F (2021) Induction of jasmonic acid biosynthetic genes inhibits Arabidopsis growth in response to low boron. J Integr Plant Biol 63(5):937\u0026ndash;948. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/jipb.13048\u003c/span\u003e\u003cspan address=\"10.1111/jipb.13048\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eJacquot A, Chaput V, Mauries A, Li Z, Tillard P, Fizames C, Bonillo P, Bellegarde F, Laugier E, Santoni V, Hem S, Martin A, Gojon A, Schulze W, Lejay L (2020) NRT2.1 C-terminus phosphorylation prevents root high affinity nitrate uptake activity in Arabidopsis thaliana. New Phytol 228(3):1038\u0026ndash;1054. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/nph.16710\u003c/span\u003e\u003cspan address=\"10.1111/nph.16710\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eJanda T, Szalai G, Pal M (2020) Salicylic Acid Signalling in Plants. Int J Mol Sci 21(7). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/ijms21072655\u003c/span\u003e\u003cspan address=\"10.3390/ijms21072655\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eKachroo P, Liu H, Kachroo A (2020) Salicylic acid: transport and long-distance immune signaling. Curr Opin Virol 42:53\u0026ndash;57. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.coviro.2020.05.008\u003c/span\u003e\u003cspan address=\"10.1016/j.coviro.2020.05.008\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eKoevoets IT, Venema JH, Elzenga JT, Testerink C (2016) Roots Withstanding their Environment: Exploiting Root System Architecture Responses to Abiotic Stress to Improve Crop Tolerance. Front Plant Sci 7:1335. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3389/fpls.2016.01335\u003c/span\u003e\u003cspan address=\"10.3389/fpls.2016.01335\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLange T, Atiq N, Pimenta Lange MJ (2023) GAS2 encodes a 2-oxoglutarate dependent dioxygenase involved in ABA catabolism. Nat Commun 14(1):7602. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41467-023-43187-1\u003c/span\u003e\u003cspan address=\"10.1038/s41467-023-43187-1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLangmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357\u0026ndash;359. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/nmeth.1923\u003c/span\u003e\u003cspan address=\"10.1038/nmeth.1923\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLi Q, Zhang X, Zhao P, Chen Y, Ni D, Wang M (2024) Metal tolerance protein CsMTP4 has dual functions in maintaining zinc homeostasis in tea plant. J Hazard Mater 471:134308. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.jhazmat.2024.134308\u003c/span\u003e\u003cspan address=\"10.1016/j.jhazmat.2024.134308\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLiao Y, Smyth GK, Shi W (2013) The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 41(10):e108. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/nar/gkt214\u003c/span\u003e\u003cspan address=\"10.1093/nar/gkt214\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLiu W, Sun J, Li J, Liu C, Si F, Yan B, Wang Z, Song X, Yang Y, Zhu Y, Cao X (2022) Reproductive tissue-specific translatome of a rice thermo-sensitive genic male sterile line. J Genet Genomics 49(7):624\u0026ndash;635. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.jgg.2022.01.002\u003c/span\u003e\u003cspan address=\"10.1016/j.jgg.2022.01.002\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLong Y, Liu Z, Jia J, Mo W, Fang L, Lu D, Liu B, Zhang H, Chen W, Zhai J (2021) FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants. Genome Biol 22(1):66. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1186/s13059-021-02288-0\u003c/span\u003e\u003cspan address=\"10.1186/s13059-021-02288-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLove MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1186/s13059-014-0550-8\u003c/span\u003e\u003cspan address=\"10.1186/s13059-014-0550-8\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541\u0026ndash;556. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1146/annurev.micro.62.081307.162918\u003c/span\u003e\u003cspan address=\"10.1146/annurev.micro.62.081307.162918\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLeeman M, Van Pelt EMDOJA, Cornelissen C, Matamala-Garros A (1996) Schippers PAHMBaB Suppression of fusarium wilt of radish by co-inoculation of fluorescent\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePseudomonas spp and root-colonizing fungi European Journal of Plant Pathology\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMao P, Duan M, Wei C, Li Y (2007) WRKY62 transcription factor acts downstream of cytosolic NPR1 and negatively regulates jasmonate-responsive gene expression. Plant Cell Physiol 48(6):833\u0026ndash;842. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/pcp/pcm058\u003c/span\u003e\u003cspan address=\"10.1093/pcp/pcm058\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMarzorati F, Rossi R, Bernardo L, Mauri P, Silvestre DD, Lauber E, Noel LD, Murgia I, Morandini P (2023) Arabidopsis thaliana Early Foliar Proteome Response to Root Exposure to the Rhizobacterium Pseudomonas simiae WCS417. Mol Plant Microbe Interact 36(11):737\u0026ndash;748. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1094/MPMI-05-23-0071-R\u003c/span\u003e\u003cspan address=\"10.1094/MPMI-05-23-0071-R\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMerchante C, Hu Q, Heber S, Alonso J, Stepanova A (2016) A Ribosome Footprinting Protocol for Plants. Bio-Protocol 6(21). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.21769/BioProtoc.1985\u003c/span\u003e\u003cspan address=\"10.21769/BioProtoc.1985\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMiao P, Wang H, Wang W, Wang Z, Ke H, Cheng H, Ni J, Liang J, Yao YF, Wang J, Zhou JM, Lei X (2025) A widespread plant defense compound disarms bacterial type III injectisome assembly. Science 387(6737):eads0377. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1126/science.ads0377\u003c/span\u003e\u003cspan address=\"10.1126/science.ads0377\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMillet YA, Danna CH, Clay NK, Songnuan W, Simon MD, Werck-Reichhart D, Ausubel FM (2010) Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell 22(3):973\u0026ndash;990. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1105/tpc.109.069658\u003c/span\u003e\u003cspan address=\"10.1105/tpc.109.069658\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMlodzinska E, Zboinska M (2016) Phosphate Uptake and Allocation - A Closer Look at Arabidopsis thaliana L. and Oryza sativa L. Front Plant Sci 7:1198. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3389/fpls.2016.01198\u003c/span\u003e\u003cspan address=\"10.3389/fpls.2016.01198\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMotte H, Vanneste S, Beeckman T (2019) Molecular and Environmental Regulation of Root Development. Annu Rev Plant Biol 70:465\u0026ndash;488. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1146/annurev-arplant-050718-100423\u003c/span\u003e\u003cspan address=\"10.1146/annurev-arplant-050718-100423\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eNakagami S, Aoyama T, Sato Y, Kajiwara T, Ishida T, Sawa S (2023) CLE3 and its homologs share overlapping functions in the modulation of lateral root formation through CLV1 and BAM1 in Arabidopsis thaliana. Plant J 113(6):1176\u0026ndash;1191. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/tpj.16103\u003c/span\u003e\u003cspan address=\"10.1111/tpj.16103\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eNakano M, Kihara M, Iehata S, Tanaka R, Maeda H, Yoshikawa T (2011) Wax ester-like compounds as biosurfactants produced by Dietzia maris from n-alkane as a sole carbon source. J Basic Microbiol 51(5):490\u0026ndash;498. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1002/jobm.201000420\u003c/span\u003e\u003cspan address=\"10.1002/jobm.201000420\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eNel B, Steinberg C, Labuschagne N, Viljoen A (2006) The potential of nonpathogenic Fusarium oxysporum and other biological control organisms for suppressing fusarium wilt of banana. Plant Pathol 55(2):217\u0026ndash;223. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/j.1365-3059.2006.01344.x\u003c/span\u003e\u003cspan address=\"10.1111/j.1365-3059.2006.01344.x\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePel MJ, Pieterse CM (2013) Microbial recognition and evasion of host immunity. J Exp Bot 64(5):1237\u0026ndash;1248. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/jxb/ers262\u003c/span\u003e\u003cspan address=\"10.1093/jxb/ers262\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePerez-Alonso MM, Guerrero-Galan C, Gonzalez Ortega-Villaizan A, Ortiz-Garcia P, Scholz SS, Ramos P, Sakakibara H, Kiba T, Ludwig-Muller J, Krapp A, Oelmuller R, Vicente-Carbajosa J, Pollmann S (2022) The calcium sensor CBL7 is required for Serendipita indica-induced growth stimulation in Arabidopsis thaliana, controlling defense against the endophyte and K(+) homoeostasis in the symbiosis. Plant Cell Environ 45(11):3367\u0026ndash;3382. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/pce.14420\u003c/span\u003e\u003cspan address=\"10.1111/pce.14420\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePetricka JJ, Clay NK, Nelson TM (2008) Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana. Plant J 56(2):251\u0026ndash;263. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/j.1365-313X.2008.03595.x\u003c/span\u003e\u003cspan address=\"10.1111/j.1365-313X.2008.03595.x\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePieterse CMJ, Berendsen RL, de Jonge R, Stringlis IA, Van Dijken AJH, Van Pelt JA, Van Wees SCM, Yu K, Zamioudis C, Bakker PAHM (2020) Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium. Plant Soil 461(1\u0026ndash;2):245\u0026ndash;263. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1007/s11104-020-04786-9\u003c/span\u003e\u003cspan address=\"10.1007/s11104-020-04786-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePratelli R, Voll LM, Horst RJ, Frommer WB, Pilot G (2010) Stimulation of nonselective amino acid export by glutamine dumper proteins. Plant Physiol 152(2):762\u0026ndash;773. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1104/pp.109.151746\u003c/span\u003e\u003cspan address=\"10.1104/pp.109.151746\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eRan LX, Liu CY, Wu GJ, van Loon LC, Bakker PAHM (2005) Suppression of bacterial wilt in Eucalyptus urophylla by fluorescent Pseudomonas spp. in China. Biol Control 32(1):111\u0026ndash;120. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.biocontrol.2004.08.007\u003c/span\u003e\u003cspan address=\"10.1016/j.biocontrol.2004.08.007\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eRen S, Li Y, Zhou Z (2025) RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data. J Genet Genomics. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.jgg.2025.04.010\u003c/span\u003e\u003cspan address=\"10.1016/j.jgg.2025.04.010\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eRuan J, Zhou Y, Zhou M, Yan J, Khurshid M, Weng W, Cheng J, Zhang K (2019) Jasmonic Acid Signaling Pathway in Plants. Int J Mol Sci 20(10). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/ijms20102479\u003c/span\u003e\u003cspan address=\"10.3390/ijms20102479\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSchenk PM, Kazan K, Rusu AG, Manners JM, Maclean DJ (2005) The SEN1 gene of Arabidopsis is regulated by signals that link plant defence responses and senescence. Plant Physiol Biochem 43(10\u0026ndash;11):997\u0026ndash;1005. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.plaphy.2005.09.002\u003c/span\u003e\u003cspan address=\"10.1016/j.plaphy.2005.09.002\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eShang E, Tu Q, Yu Z, Ding Z (2025) Cell wall dynamic changes and signaling during plant lateral root development. J Integr Plant Biol 67(3):632\u0026ndash;648. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/jipb.13844\u003c/span\u003e\u003cspan address=\"10.1111/jipb.13844\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eShidore T, Triplett LR (2017) Toxin-Antitoxin Systems: Implications for Plant Disease. Annu Rev Phytopathol 55:161\u0026ndash;179. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1146/annurev-phyto-080516-035559\u003c/span\u003e\u003cspan address=\"10.1146/annurev-phyto-080516-035559\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSong J-M, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie W-Z, Cheng Y, Zhang Y, Liu K, Yang Q-Y, Chen L-L, Guo L (2020) Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants 6(1):34\u0026ndash;45. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41477-019-0577-7\u003c/span\u003e\u003cspan address=\"10.1038/s41477-019-0577-7\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eStringlis IA, Proietti S, Hickman R, Van Verk MC, Zamioudis C, Pieterse CMJ (2018) Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists. Plant J 93(1):166\u0026ndash;180. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/tpj.13741\u003c/span\u003e\u003cspan address=\"10.1111/tpj.13741\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSu YH, Frommer WB, Ludewig U (2004) Molecular and functional characterization of a family of amino acid transporters from Arabidopsis. Plant Physiol 136(2):3104\u0026ndash;3113. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1104/pp.104.045278\u003c/span\u003e\u003cspan address=\"10.1104/pp.104.045278\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eTao L, Wang L, Liu L, Cheng X, Zhang Q (2024) Phosphorous accumulation associated with mitochondrial PHT3-mediated enhanced arsenate tolerance in Chlamydomonas reinhardtii. J Hazard Mater 478:135460. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.jhazmat.2024.135460\u003c/span\u003e\u003cspan address=\"10.1016/j.jhazmat.2024.135460\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eVacheron J, Desbrosses G, Renoud S, Padilla R, Walker V, Muller D, Prigent-Combaret C (2018) Differential Contribution of Plant-Beneficial Functions from Pseudomonas kilonensis F113 to Root System Architecture Alterations in Arabidopsis thaliana and Zea mays. Mol Plant Microbe Interact 31(2):212\u0026ndash;223. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1094/MPMI-07-17-0185-R\u003c/span\u003e\u003cspan address=\"10.1094/MPMI-07-17-0185-R\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003evan Loon LC, Geraats BP, Linthorst HJ (2006) Ethylene as a modulator of disease resistance in plants. Trends Plant Sci 11(4):184\u0026ndash;191. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.tplants.2006.02.005\u003c/span\u003e\u003cspan address=\"10.1016/j.tplants.2006.02.005\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eVerbon EH, Liberman LM (2016) Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development. Trends Plant Sci 21(3):218\u0026ndash;229. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.tplants.2016.01.013\u003c/span\u003e\u003cspan address=\"10.1016/j.tplants.2016.01.013\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eVerbon EH, Trapet PL, Kruijs S, Temple-Boyer-Dury C, Rouwenhorst TG, Pieterse CMJ (2019) Rhizobacteria-Mediated Activation of the Fe Deficiency Response in Arabidopsis Roots: Impact on Fe Status and Signaling. Front Plant Sci 10:909. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3389/fpls.2019.00909\u003c/span\u003e\u003cspan address=\"10.3389/fpls.2019.00909\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eVerbon EH, Trapet PL, Stringlis IA, Kruijs S, Bakker P, Pieterse CMJ (2017) Iron and Immunity. Annu Rev Phytopathol 55:355\u0026ndash;375. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1146/annurev-phyto-080516-035537\u003c/span\u003e\u003cspan address=\"10.1146/annurev-phyto-080516-035537\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eVorwerk S, Schiff C, Santamaria M, Koh S, Nishimura M, Vogel J, Somerville C, Somerville S (2007) EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana. BMC Plant Biol 7:35. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1186/1471-2229-7-35\u003c/span\u003e\u003cspan address=\"10.1186/1471-2229-7-35\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eVyse K, Schaarschmidt S, Erban A, Kopka J, Zuther E (2022) Specific CBF transcription factors and cold-responsive genes fine-tune the early triggering response after acquisition of cold priming and memory. Physiol Plant 174(4):e13740. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/ppl.13740\u003c/span\u003e\u003cspan address=\"10.1111/ppl.13740\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWang T, Cui Y, Jin J, Guo J, Wang G, Yin X, He QY, Zhang G (2013) Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific. Nucleic Acids Res 41(9):4743\u0026ndash;4754. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/nar/gkt178\u003c/span\u003e\u003cspan address=\"10.1093/nar/gkt178\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWang W, Bai XD, Chen K, Zhang XY, Gu CR, Jiang J, Yang CP, Liu GF (2022) PsnWRKY70 Negatively Regulates NaHCO(3) Tolerance in Populus. Int J Mol Sci 23(21). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/ijms232113086\u003c/span\u003e\u003cspan address=\"10.3390/ijms232113086\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWang Z, Song Y (2022) Toward understanding the genetic bases underlying plant-mediated cry for help to the microbiota. Imeta 1(1):e8. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1002/imt2.8\u003c/span\u003e\u003cspan address=\"10.1002/imt2.8\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWu HL, Jen J, Hsu PY (2024) What, where, and how: Regulation of translation and the translational landscape in plants. Plant Cell 36(5):1540\u0026ndash;1564. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/plcell/koad197\u003c/span\u003e\u003cspan address=\"10.1093/plcell/koad197\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYang Q, Li Z, Guan K, Wang Z, Tang X, Hong Y, Liu Z, Zhai J, Huang A, Long Y, Song Y (2025) Comparative single-nucleus RNA-seq analysis revealed localized and cell type-specific pathways governing root-microbiome interactions. Nat Commun 16(1):3169. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41467-025-58395-0\u003c/span\u003e\u003cspan address=\"10.1038/s41467-025-58395-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYang TH, Lenglet-Hilfiker A, Stolz S, Glauser G, Farmer EE (2020) Jasmonate Precursor Biosynthetic Enzymes LOX3 and LOX4 Control Wound-Response Growth Restriction. Plant Physiol 184(2):1172\u0026ndash;1180. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1104/pp.20.00471\u003c/span\u003e\u003cspan address=\"10.1104/pp.20.00471\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYang Z, Wang S, Wei L, Huang Y, Liu D, Jia Y, Luo C, Lin Y, Liang C, Hu Y, Dai C, Guo L, Zhou Y, Yang Q-Y (2023) BnIR: A multi-omics database with various tools for Brassica napus research and breeding. Mol Plant 16(4):775\u0026ndash;789. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.molp.2023.03.007\u003c/span\u003e\u003cspan address=\"10.1016/j.molp.2023.03.007\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYu K, Liu Y, Tichelaar R, Savant N, Lagendijk E, van Kuijk SJL, Stringlis IA, van Dijken AJH, Pieterse CMJ, Bakker P, Haney CH, Berendsen RL (2019a) Rhizosphere-Associated Pseudomonas Suppress Local Root Immune Responses by Gluconic Acid-Mediated Lowering of Environmental pH. Curr Biol 29(22):3913\u0026ndash;3920e3914. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.cub.2019.09.015\u003c/span\u003e\u003cspan address=\"10.1016/j.cub.2019.09.015\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYu K, Pieterse CMJ, Bakker P, Berendsen RL (2019b) Beneficial microbes going underground of root immunity. Plant Cell Environ 42(10):2860\u0026ndash;2870. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/pce.13632\u003c/span\u003e\u003cspan address=\"10.1111/pce.13632\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYu Z, Qu X, Lv B, Li X, Sui J, Yu Q, Ding Z (2024) MAC3A and MAC3B mediate degradation of the transcription factor ERF13 and thus promote lateral root emergence. Plant Cell 36(9):3162\u0026ndash;3176. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1093/plcell/koae047\u003c/span\u003e\u003cspan address=\"10.1093/plcell/koae047\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZamioudis C, Hanson J, Pieterse CM (2014) beta-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots. New Phytol 204(2):368\u0026ndash;379. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/nph.12980\u003c/span\u003e\u003cspan address=\"10.1111/nph.12980\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZamioudis C, Korteland J, Van Pelt JA, van Hamersveld M, Dombrowski N, Bai Y, Hanson J, Van Verk MC, Ling HQ, Schulze-Lefert P, Pieterse CM (2015) Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses. Plant J 84(2):309\u0026ndash;322. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/tpj.12995\u003c/span\u003e\u003cspan address=\"10.1111/tpj.12995\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZamioudis C, Mastranesti P, Dhonukshe P, Blilou I, Pieterse CM (2013) Unraveling root developmental programs initiated by beneficial Pseudomonas spp. bacteria. Plant Physiol 162(1):304\u0026ndash;318. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1104/pp.112.212597\u003c/span\u003e\u003cspan address=\"10.1104/pp.112.212597\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZarei A, Brikis CJ, Bajwa VS, Chiu GZ, Simpson JP, DeEll JR, Bozzo GG, Shelp BJ (2017) Plant Glyoxylate/Succinic Semialdehyde Reductases: Comparative Biochemical Properties, Function during Chilling Stress, and Subcellular Localization. Front Plant Sci 8:1399. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3389/fpls.2017.01399\u003c/span\u003e\u003cspan address=\"10.3389/fpls.2017.01399\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZhang J, Liu W, Bu J, Lin Y, Bai Y (2023) Host genetics regulate the plant microbiome. Curr Opin Microbiol 72:102268. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.mib.2023.102268\u003c/span\u003e\u003cspan address=\"10.1016/j.mib.2023.102268\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZhao Z, Fan J, Gao YG, Wang Z, Yang P, Liang Y, Opiyo S, Xia Y (2022) Arabidopsis Plasma Membrane ATPase AHA5 Is Negatively Involved in PAMP-Triggered Immunity. Int J Mol Sci 23(7). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/ijms23073857\u003c/span\u003e\u003cspan address=\"10.3390/ijms23073857\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZhong R, Lee C, Zhou J, McCarthy RL, Ye ZH (2008) A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20(10):2763\u0026ndash;2782. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1105/tpc.108.061325\u003c/span\u003e\u003cspan address=\"10.1105/tpc.108.061325\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZhou J, Uribe Acosta M, Stassen MJJ, Qi R, de Jonge R, White F, Kramer G, Dong L, Pieterse CMJ, Stringlis IA (2025) Arabidopsis root defense barriers support beneficial interactions with rhizobacterium Pseudomonas simiae WCS417. New Phytol. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1111/nph.70549\u003c/span\u003e\u003cspan address=\"10.1111/nph.70549\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"molecular-breeding","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"molb","sideBox":"Learn more about [Molecular Breeding](https://www.springer.com/journal/11032)","snPcode":"11032","submissionUrl":"https://submission.nature.com/new-submission/11032/3","title":"Molecular Breeding","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-7990582/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7990582/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eInteractions between plant roots and complex microbial communities are critical for plant environmental adaptation. \u003cem\u003ePseudomonas simiae\u003c/em\u003e WCS417, a Gram-negative plant growth-promoting rhizobacterium (PGPR), is a model organism in plant-microbe interaction research and featured in over 750 studies since the 1990s. However, the translatome dynamics induced by WCS417 remain poorly understood. This study employed an integrated multi-omics approach, combining transcriptome (RNA-seq) and translatome (RNC-seq) analyses, to systematically investigate the transcriptional and translational regulatory networks in \u003cem\u003eBrassica napus\u003c/em\u003e roots during early colonization by WCS417. Our results demonstrate that WCS417 significantly promotes lateral root formation, suppresses primary root elongation, and increases plant biomass. At the molecular level, WCS417 inoculation triggered extensive changes in gene expression and translation at 30 minutes and 6 hours post-inoculation, affecting key processes including phytohormone signaling, cell wall remodeling, immune responses, and abiotic stress adaptation. Notably, although transcript levels of some immune-related genes were downregulated, their translation efficiency was significantly enhanced, suggesting that plants maintain basal immunity while facilitating symbiotic establishment. Furthermore, WCS417 dynamically regulated genes involved in nitrogen/phosphorus uptake and core low-temperature response transcription factors in \u003cem\u003eBrassica napus\u003c/em\u003e roots. These findings reveal a multi-layered regulatory mechanism by which WCS417 optimizes root system architecture and balances immunity with growth in \u003cem\u003eBrassica napus\u003c/em\u003e, providing new insights into plant-microbe interactions.\u003c/p\u003e","manuscriptTitle":"Integrated transcriptome and translatome analyses reveal the early regulatory network of Brassica napus roots in response to the growth-promoting rhizobacterium Pseudomonas simiae WCS417","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-13 19:58:27","doi":"10.21203/rs.3.rs-7990582/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-11-18T04:14:39+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-15T08:52:26+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-11T04:49:27+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"310108767801395684361639250531326598523","date":"2025-11-03T12:18:46+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"154880543225189333046507608446974337073","date":"2025-11-03T11:33:49+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-11-03T11:19:23+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-11-03T11:06:44+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-10-31T00:24:25+00:00","index":"","fulltext":""},{"type":"submitted","content":"Molecular Breeding","date":"2025-10-30T14:41:16+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"molecular-breeding","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"molb","sideBox":"Learn more about [Molecular Breeding](https://www.springer.com/journal/11032)","snPcode":"11032","submissionUrl":"https://submission.nature.com/new-submission/11032/3","title":"Molecular Breeding","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"55eb637a-754c-4514-b738-caa27314ab09","owner":[],"postedDate":"November 13th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-01-19T16:49:53+00:00","versionOfRecord":{"articleIdentity":"rs-7990582","link":"https://doi.org/10.1007/s11032-025-01628-3","journal":{"identity":"molecular-breeding","isVorOnly":false,"title":"Molecular Breeding"},"publishedOn":"2026-01-12 16:30:47","publishedOnDateReadable":"January 12th, 2026"},"versionCreatedAt":"2025-11-13 19:58:27","video":"","vorDoi":"10.1007/s11032-025-01628-3","vorDoiUrl":"https://doi.org/10.1007/s11032-025-01628-3","workflowStages":[]},"version":"v1","identity":"rs-7990582","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7990582","identity":"rs-7990582","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}