scholarly journals Choosing reference genes for RT-qPCR for Fusarium graminearum plant infection (In Planta) and In Vitro growth studies based on transcriptomic data

2019 ◽  
Author(s):  
Xiaorong Lin ◽  
Hongchen Li ◽  
Zonghua Wang ◽  
Stefan Olsson
Keyword(s):  
Fusarium Graminearum ◽  
Reference Genes ◽  
Target Genes ◽  
Housekeeping Genes ◽  
Relative Difference ◽  
Transcriptome Data ◽  
In Planta ◽  
Plant Infection ◽  
Selection Of

Background. Choosing reference genes for RT-qPCR for the study of transcriptomic responses of target genes is often done using “standard” reference genes (housekeeping genes) selected before the genomic era. Now, published transcriptome data can be used to aid in this selection to avoid the selection of a reference gene that varies and obscure results. Methods. We use transcriptome data for the model pathogen fungus Fusarium graminearum to select housekeeping genes for In Vitro and In Planta conditions. Transcriptome data was downloaded from a publicly available database. We selected a database where transcriptome chip data from many experiments using the same chip has been deposited divided the downloaded data into In Vitro and In Planta conditions based on the information about the experiments. Results. We ranked the genes with the least variation (relative difference between maximum and minimum expression) across each dataset. Genes previously shown to perform well as reference genes for In Vitro conditions in a similar analysis as ours also performed well for In Vitro conditions in our dataset but worked less well for In Planta conditions. We found 5 reference genes that performed well under both In Planta conditions and In Vitro conditions. Discussion. Even if these 5 reference genes performed well, for other (new) target conditions we recommend making a transcriptome analysis to select well performing reference genes for RT-qPCR if possible. Alternatively, select 2 of the 5 genes that we show here performed well under both In Planta and In Vitro conditions.

scholarly journals Choosing reference genes for RT-qPCR for Fusarium graminearum plant infection (In Planta) and In Vitro growth studies based on transcriptomic data

2019 ◽  
Author(s):  
Xiaorong Lin ◽  
Hongchen Li ◽  
Zonghua Wang ◽  
Stefan Olsson
Keyword(s):  
Fusarium Graminearum ◽  
Reference Genes ◽  
Target Genes ◽  
Housekeeping Genes ◽  
Relative Difference ◽  
Transcriptome Data ◽  
In Planta ◽  
Plant Infection ◽  
Selection Of

Background. Choosing reference genes for RT-qPCR for the study of transcriptomic responses of target genes is often done using “standard” reference genes (housekeeping genes) selected before the genomic era. Now, published transcriptome data can be used to aid in this selection to avoid the selection of a reference gene that varies and obscure results. Methods. We use transcriptome data for the model pathogen fungus Fusarium graminearum to select housekeeping genes for In Vitro and In Planta conditions. Transcriptome data was downloaded from a publicly available database. We selected a database where transcriptome chip data from many experiments using the same chip has been deposited divided the downloaded data into In Vitro and In Planta conditions based on the information about the experiments. Results. We ranked the genes with the least variation (relative difference between maximum and minimum expression) across each dataset. Genes previously shown to perform well as reference genes for In Vitro conditions in a similar analysis as ours also performed well for In Vitro conditions in our dataset but worked less well for In Planta conditions. We found 5 reference genes that performed well under both In Planta conditions and In Vitro conditions. Discussion. Even if these 5 reference genes performed well, for other (new) target conditions we recommend making a transcriptome analysis to select well performing reference genes for RT-qPCR if possible. Alternatively, select 2 of the 5 genes that we show here performed well under both In Planta and In Vitro conditions.

scholarly journals Small RNA bidirectional crosstalk during the interaction between wheat andZymoseptoria tritici

2018 ◽  
Author(s):  
Xin Ma ◽  
Nicolas Bologna ◽  
Javier Palma-Guerrero
Keyword(s):  
Fungal Infection ◽  
Target Genes ◽  
In Planta ◽  
Zymoseptoria Tritici ◽  
Plant Infection ◽  
Gene Transcripts ◽  
Plant Pathogen Interactions ◽  
Lower Expression

AbstractCross-kingdom RNAi has been shown to play important roles during plant pathogen interactions. But this cross-kingdom RNAi was still unexplored in the wheat-Zymoseptoria triticipathosystem. Here we performed a detailed analysis of the sRNA bidirectional crosstalk between wheat andZ.tritici. Using a combination of sRNA-seq and mRNA-seq we were able to identify known and novel sRNAs and study their expression and their action on putative targets in both wheat andZ.tritici. We predicted the target genes of all the sRNAs in either wheat orZ.triticitranscriptome and used degradome analysis to validate the cleavage of these gene transcripts. We could not find any clear evidence of a cross-kingdom RNAi in this pathosystem. We also found that the fungal sRNA enrichment was lowerin plantathan duringin vitrogrowth, probably due to the lower expression of the only Dicer gene of the fungus during plant infection. However, we found a downregulation of specific wheat sRNAs during the fungal infection, leading to a boost expression of wheat defense related genes, which may be enhancing the plant defense ability against the pathogen. Additionally, the fungal infection also induced sRNAs regulating the expression of specific wheat genes, including auxin related genes, as an immune response. These results confirm the role of sRNAs in the regulation of wheat defenses duringZ.triticiinfection. Our findings contribute to improve our understanding of the interactions between wheat andZ.tritici.

scholarly journals Peroxisome Function Is Required for Virulence and Survival of Fusarium graminearum

2012 ◽  
Vol 25 (12) ◽  
pp. 1617-1627 ◽  
Author(s):  
Kyunghun Min ◽  
Hokyoung Son ◽  
Jungkwan Lee ◽  
Gyung Ja Choi ◽  
Jin-Cheol Kim ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fusarium Graminearum ◽  
Protein Import ◽  
Fluorescent Proteins ◽  
Deletion Mutants ◽  
In Planta ◽  
Peroxisomal Protein ◽  
Peroxisomal Targeting ◽  
Signal Type

Peroxisomes are organelles that are involved in a number of important cellular metabolic processes, including the β-oxidation of fatty acids, biosynthesis of secondary metabolites, and detoxification of reactive oxygen species (ROS). In this study, the role of peroxisomes was examined in Fusarium graminearum by targeted deletion of three genes (PEX5, PEX6, and PEX7) encoding peroxin (PEX) proteins required for peroxisomal protein import. PEX5 and PEX7 deletion mutants were unable to localize the fluorescently tagged peroxisomal targeting signal type 1 (PTS1)- and PTS2-containing proteins to peroxisomes, respectively, whereas the PEX6 mutant failed to localize both fluorescent proteins. Deletion of PEX5 and PEX6 resulted in retarded growth on long-chain fatty acids and butyrate, while the PEX7 deletion mutants utilized fatty acids other than butyrate. Virulence on wheat heads was greatly reduced in the PEX5 and PEX6 deletion mutants, and they were defective in spreading from inoculated florets to the adjacent spikelets through rachis. Deletion of PEX5 and PEX6 dropped survivability of aged cells in planta and in vitro due to the accumulation of ROS followed by necrotic cell death. These results demonstrate that PTS1-dependent peroxisomal protein import mediated by PEX5 and PEX6 are critical to virulence and survival of F. graminearum.

scholarly journals Cinnamic-Derived Acids Significantly Affect Fusarium graminearum Growth and In Vitro Synthesis of Type B Trichothecenes

2011 ◽  
Vol 101 (8) ◽  
pp. 929-934 ◽  
Author(s):  
Nadia Ponts ◽  
Laetitia Pinson-Gadais ◽  
Anne-Laure Boutigny ◽  
Christian Barreau ◽  
Florence Richard-Forget
Keyword(s):  
Fusarium Graminearum ◽  
Phenolic Acids ◽  
Antioxidant Properties ◽  
Fungal Growth ◽  
Type B ◽  
In Planta ◽  
In Vitro Synthesis ◽  
The Impact ◽  
Toxin Accumulation

The impact of five phenolic acids (ferulic, coumaric, caffeic, syringic, and p-hydroxybenzoic acids) on fungal growth and type B trichothecene production by four strains of Fusarium graminearum was investigated. All five phenolic acids inhibited growth but the degree of inhibition varied between strains. Our results suggested that the more lipophilic phenolic acids are, the higher is the effect they have on growth. Toxin accumulation in phenolic acid-supplemented liquid glucose, yeast extract, and peptone cultures was enhanced in the presence of ferulic and coumaric acids but was reduced in the presence of p-hydroxybenzoic acid. This modulation was shown to correlate with a regulation of TRI5 transcription. In this study, addition of phenolic acids with greater antioxidant properties resulted in a higher toxin accumulation, indicating that the modulation of toxin accumulation may be linked to the antioxidant properties of the phenolic acids. These data suggest that, in planta, different compositions in phenolic acids of kernels from various cultivars may reflect different degrees of sensitivity to “mycotoxinogenesis.”

scholarly journals Expression Analysis of XTH in Stem Swelling of Stem Mustard and Selection of Reference Genes

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 113 ◽  
Author(s):  
Mengyao Li ◽  
Fangjie Xie ◽  
Qi He ◽  
Jie Li ◽  
Jiali Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Expression Patterns ◽  
Regulatory Mechanisms ◽  
Future Research ◽  
Transcriptome Data ◽  
Accurate Analysis ◽  
Report Analysis ◽  
The Stability ◽  
Selection Of

Accurate analysis of gene expression requires selection of appropriate reference genes. In this study, we report analysis of eight candidate reference genes (ACTIN, UBQ, EF-1α, UBC, IF-4α, TUB, PP2A, and HIS), which were screened from the genome and transcriptome data in Brassica juncea. Four statistical analysis softwares geNorm, NormFinder, BestKeeper, and RefFinder were used to test the reliability and stability of gene expression of the reference genes. To further validate the stability of reference genes, the expression levels of two CYCD3 genes (BjuB045330 and BjuA003219) were studied. In addition, all genes in the xyloglucan endotransglucosylase/hydrolase (XTH) family were identified in B. juncea and their patterns at different periods of stem enlargement were analyzed. Results indicated that UBC and TUB genes showed stable levels of expression and are recommended for future research. In addition, XTH genes were involved in regulation of stem enlargement expression. These results provide new insights for future research aiming at exploring important functional genes, their expression patterns and regulatory mechanisms for mustard development.

Endophytic fungi as a promising biocontrol agent to protect wheat from Fusarium graminearum head blight

Plant Disease ◽  
2021 ◽  
Author(s):  
Zachary Albert Noel ◽  
Ludmilla Roze ◽  
Mikaela Breunig ◽  
Frances Trail
Keyword(s):  
Microbial Community ◽  
Fusarium Graminearum ◽  
Endophytic Fungi ◽  
Seed Weight ◽  
Biocontrol Agent ◽  
Fungal Endophytes ◽  
In Planta ◽  
Head Blight ◽  
Species Definitions

The search for beneficial endophytes that can be part of a constructed microbial community has increased in recent years. We characterized three endophytic fungi previously isolated from wheat for their in vitro and in planta antagonism toward the Fusarium head blight pathogen, Fusarium graminearum. The endophytes were phylogenetically characterized and shown to be Alternaria destruens, Fusarium commune, and Fusarium oxysporum. Individual fungal endophytes significantly increased seed weight and lowered the accumulation of the mycotoxin deoxynivalenol compared to F. graminearum infected wheat heads without endophyte pretreatment. Investigation into the mechanism of competition in vitro showed that endophytes competitively excluded F. graminearum by pre-emptive colonization and possible inhibition over a distance. Investigations on the use of these endophytes in the field are in progress. Identification of these three endophytes highlights a common quandary in searching for beneficial microbes to use in agriculture: species definitions often do not separate individual isolates’ lifestyles. A greater understanding of the risks in using intraspecies variants for biocontrol is needed and should be examined in the context of the ecology of the individuals being investigated.

scholarly journals Fungal Endophytes Control Fusarium graminearum and Reduce Trichothecenes and Zearalenone in Maize

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 493 ◽  
Author(s):  
Mohamed F. Abdallah ◽  
Marthe De Boevre ◽  
Sofie Landschoot ◽  
Sarah De Saeger ◽  
Geert Haesaert ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Fusarium Graminearum ◽  
Fungal Endophytes ◽  
Agricultural Science ◽  
Ear Rot ◽  
Seedling Blight ◽  
In Planta ◽  
Detoxification Mechanisms ◽  
Comparative Trials

Fusarium graminearum can cause Giberella Ear Rot (GER) and seedling blight in maize, resulting in major yield losses. Besides GER, the infected grains are consequently contaminated with multiple mycotoxins of F. graminearum. Zearalenone and trichothecenes, such as deoxynivalenol and its acetylated forms, are among the major mycotoxins associated with F. graminearum infection in maize. In the current work, we explored the effect of the endophytic fungal genera of Epicoccum and Sordaria, to control F. graminearum infection in comparative trials with Piriformospora spp., an elusive endophytic genus. Furthermore, we investigated the effect of these endophytes on zearalenone, deoxynivalenol, and 15-acetyldeoxynivalenol levels using in vitro and in planta assays. As plants are endowed with several detoxification mechanisms comprising e.g., glucosylation of trichothecenes, the effect of the isolated fungal endophytes on the deoxynivalenol-3-glucoside level was also assessed. In general, results showed a considerable variability in the antifungal activity, both among species and among isolates within one species. Additionally, the effect on mycotoxin levels was variable, and not necessarily related to the antifungal activity except for zearalenone levels which were consistently reduced by the endophytes. These results highlight the great potential of certain endophytic fungal strains as new biocontrol agents in agricultural science.

scholarly journals Toxigenic Capacity and Trichothecene Production by Fusarium graminearum Isolates from Argentina and Their Relationship with Aggressiveness and Fungal Expansion in the Wheat Spike

2014 ◽  
Vol 104 (4) ◽  
pp. 357-364 ◽  
Author(s):  
I. Malbrán ◽  
C. A. Mourelos ◽  
J. R. Girotti ◽  
P. A. Balatti ◽  
G. A. Lori
Keyword(s):  
Fusarium Graminearum ◽  
Vascular Tissue ◽  
Close Correlation ◽  
Field Trials ◽  
In Planta ◽  
Head Blight ◽  
Variable Intensity ◽  
Polymerase Chain

At least 20 epidemics of Fusarium head blight (FHB) of wheat have been registered in the last 50 years in Argentina, with variable intensity. Damage induced by the disease is further aggravated by the presence of mycotoxins in affected grains that may cause health problems to humans and animals. The trichothecene chemotype was analyzed for 112 isolates of Fusarium graminearum from Argentina by polymerase chain reaction and two field trials were conducted to study the aggressiveness of a subsample of 14 representative isolates and to analyze deoxynivalenol (DON) production in planta and in vitro. All isolates belonged to the 15-acetyl-DON chemotype. Significant differences were observed in both the symptom severity induced in wheat spikes and the in vivo DON production, and a close correlation was found between these two variables. However, in vitro toxigenic potential was not correlated with the capacity of F. graminearum isolates to produce DON under natural conditions. The progress of infection in the rachis of inoculated wheat spikes was analyzed and the pathogen presence verified in both symptomatic and symptomless spikes. Even isolates with a limited capacity to induce symptoms were able to colonize the vascular tissue and to produce considerable amounts of DON in planta.

scholarly journals The Fusarium graminearum t-SNARE Sso2 Is Involved in Growth, Defense, and DON Accumulation and Virulence

2020 ◽  
Vol 33 (7) ◽  
pp. 888-901
Author(s):  
Sean P. O’Mara ◽  
Karen Broz ◽  
Marike Boenisch ◽  
Zixuan Zhong ◽  
Yanhong Dong ◽  
...  
Keyword(s):  
Fusarium Graminearum ◽  
Deletion Mutant ◽  
Expression Profiles ◽  
Pathogenic Fungus ◽  
Gene Expression Profiles ◽  
Plant Diseases ◽  
In Planta ◽  
Head Blight ◽  
Double Deletion

The plant-pathogenic fungus Fusarium graminearum, causal agent of Fusarium head blight (FHB) disease on small grain cereals, produces toxic trichothecenes that require facilitated export for full virulence. Two potential modes of mycotoxin transport are membrane-bound transporters, which move toxins across cellular membranes, and N-ethylmaleimide-sensitive factor attachment receptor (SNARE)-mediated vesicular transport, by which toxins may be packaged as cargo in vesicles bound for organelles or the plasma membrane. In this study, we show that deletion of a gene (Sso2) for a subapically localized t-SNARE protein results in growth alteration, increased sensitivity to xenobiotics, altered gene expression profiles, and reduced deoxynivalenol (DON) accumulation in vitro and in planta as well as reduced FHB symptoms on wheat. A double deletion mutant generated by crossing the ∆sso2 deletion mutant with an ATP-binding cassette transporter deletion mutant (∆abc1) resulted in an additive reduction in DON accumulation and almost complete loss of FHB symptoms in planta. These results suggest an important role of Sso2-mediated subapical exocytosis in FHB progression and xenobiotic defense and are the first report of an additive reduction in F. graminearum DON accumulation upon deletion of two distinct modes of cellular export. This research provides useful information which may aid in formulating novel management plans of FHB or other destructive plant diseases.

Sign in / Sign up

Export Citation Format

Share Document