Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA278121: Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum

Source: NCBI / GSE66861
Submission Date: Mar 13 2015
Release Date: Mar 31 2016
Update Date: May 15 2019

Summary: 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.

Overall Design: 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.

GEN Datasets:
GEND000271
Strategy:
Species:
Tissue:
Isolation_source:
Development Stage:
Protocol
Growth Protocol: Inoculum for both isolates was grown for seven days on potato dextrose agar (PDA) at 25 °C with a 12-h photoperiod. Conidia were collected by rinsing plates with sterile water, scraping the agar surface with a scalpel and filtering the conidial suspension through sterile cloth. Spore suspension was adjusted to a final concentration of 1 × 106 conidia/ml based on microscopic counts using a Bürker chamber. Fifteen seeds of the partially resistant Forrest genotype were placed on a paper towel moistened with sterile distilled water and inoculated by pipette with 100 μl of 1 × 106 conidial suspension of FO36 or FO40 isolates. Another moistened paper towel was placed over the inoculated seeds, rolled up, and placed vertically in a 25-l bucket. An open plastic bag was placed over each towel to avoid cross-contamination between isolates. A black plastic bag was placed over each bucket and they were placed on a bench at room temperature (~22 °C). Noninoculated checks were included to ensure that other seed pathogens were not present. For RNA-Seq analysis, roots were collected at 72 and 96 hpi. Noninoculated control roots were sampled at the same times listed above. Three pools of five roots were prepared for each isolate and sampling time. The resulting samples were immediately frozen in liquid nitrogen and stored at -80 °C until biological analysis were carried out.
Treatment Protocol: Soybean [G. max (L.) Merrill] partially resistant genotype Forrest was evaluated after inoculation with a conidial suspension of non-pathogenic FO36 and pathogenic FO40 F. oxysporum isolates.
Extract Protocol: Soybean seedlings were collected, flash frozen on liquid nitrogen, and RNA was extracted using Trizol reagent.
Library Construction Protocol: RNA libraries were prepared for sequencing using standard Illumina protocols
Sequencing
Molecule Type: -
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum.
BMC genomics . 2015-12-21 [PMID: 26689712]