Dataset Information

P. sojae apoplastic effectors in soybean apoplastic fluid at different infection time points.

ABSTRACT: Soybean leaves were inoculated with P. sojae strain P6497, and apoplastic fluid was collected at 1.5, 3, and 6 hours post-inoculation (hpi). The samples were analyzed using MS to identify candidate apoplastic effectors and PsTry1.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Phytophthora Sojae Strain P6497

SUBMITTER: Sicong Zhang

LAB HEAD: Yuanchao Wang

PROVIDER: PXD058375 | Pride | 2025-06-14

REPOSITORIES: Pride

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Project description:Some strains of the foliar pathogen Pseudomonas syringae are adapted for growth and survival on leaf surfaces and in the leaf interior. Global transcriptome profiling was used to evaluate if these two habitats offer distinct environments for bacteria and thus present distinct driving forces for adaptation. Further transcriptome profiling was performed to understand the various environmental conditions that P. syringae cells encounter during their association with plants. RNA was collected from P. syringae pv. syringae strain B728a cells that were exposed to seven treatments. The treatments included five in vitro treatments, namely exposing cells to a basal medium, sodium chloride to confer an osmotic stress, hydrogen peroxide to confer an apoplastic growth, iron limitation, nitrogen limitation. They also included two in planta treatments, namely recovering cells from epiphytic sites after surface inoculation and 72 h of growth on bean (Phaseolus vulgaris L.) leaves and recovering cells from apoplastic sites after infiltration and 48 h of growth in bean leaves. The results suggested that B728a cells experience vastly different environments when growing on the surface versus the interior of leaves and identified distinct traits that are likely used for persistence and growth in these environments. RNA was collected from B728a cells that were exposed to seven treatments, each with two biological replicates in each of three laboratories. Experimental methods were standardized across the three laboratories. For the in vitro treatments, exponential cells from two independent cultures were each exposed to the five treatments. For each treatment, the cells originating from the two cultures were pooled and the RNA was extracted; this was repeated in its entirety and the two RNA pools were combined. The resulting RNA representing four independent cultures served as a single biological replicate. Two biological replicates for each treatment were generated in this manner in each of three separate laboratories. Epiphytic B728a populations were established following spray inoculation onto bean leaves and subsequent incubation; the epiphytic cells recovered from 400 to 600 leaves inoculated at one time served as a biological replicate, and the procedure was repeated to provide two biological replicates. Due to the availability of facilities, all of the epiphytic treatments were conducted at as single laboratory, with cultures provided from each of the other laboratories, and the cell pellets were returned to those laboratories for RNA extraction and analysis. Apoplastic B728a populations were established following vacuum infiltration into bean leaves and subsequent incubation; the apoplastic cells recovered from 40 to 80 leaves inoculated at one time served as a biological replicate, and two biological replicates were generated at each of the three laboratories. The RNA from all treatments was submitted to Roche Nimblegen, Inc where it was labeled and hybridized to an ORF-based microarray that included 5,071 ORFs and 61 putative sRNAs, with each ORF represented by 14 60-mer nucleotide probes. The fluorescence intensity for each probe was measured and subjected to robust multiarray averaging, which included adjustment for the background intensity, log2 transformation, quantile normalization and median polishing, and a robust estimated mean value was determined for each ORF and putative sRNA on the array.

Project description:Fusarium oxysporum is one of the most common species causing soybean root rot and seedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the first time to investigate the molecular aspect of the interaction of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post inoculation (hpi). Markedly different gene expression profiles were observed in compatible and incompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was observed at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was about eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of many well-known defense-related genes, and several genes involved in ethylene biosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition, 1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during the infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes, reactive oxygen species-related enzymes and fungal proteins involved in primary metabolic pathways. Such information may be useful in the development of new methods of broadening resistance of soybean to F. oxysporum, including the silencing of important fungal genes, and also to understand the molecular basis of soybean-F. oxysporum interactions. Soybean seedlings mRNA profiles inoculated with a non-pathogenic and pathogenic isolates of F. oxysporum and collected at 72 and 96 hpi, were generated using Illumina HiSeq 2500. Control seedlings were also included for each time of inoculation. Three biological replicates were considered for each condition, 18 samples in total.

			Action	DRS
	180min.txt	Txt
	360min.txt	Txt
	90min.txt	Txt
	Ps_180min.mzML	Mzml
	Ps_360min.mzML	Mzml

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P. sojae apoplastic effectors in soybean apoplastic fluid at different infection time points.

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