Identification of Differentially Expressed Fungal Genes In Planta by Suppression Subtraction Hybridization

2010 ◽  
pp. 115-123 ◽  
Author(s):  
Benjamin A. Horwitz ◽  
Sophie Lev
Keyword(s):  
Differentially Expressed ◽  
In Planta ◽  
Suppression Subtraction Hybridization ◽  
Subtraction Hybridization ◽  
Fungal Genes

scholarly journals Identification of differentially expressed and developmentally regulated genes in medulloblastoma using suppression subtraction hybridization

Oncogene ◽  
2004 ◽  
Vol 23 (19) ◽  
pp. 3444-3453 ◽  
Author(s):  
Naoki Yokota ◽  
Todd G Mainprize ◽  
Michael D Taylor ◽  
Tomohiko Kohata ◽  
Michael Loreto ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Developmentally Regulated ◽  
Suppression Subtraction Hybridization ◽  
Subtraction Hybridization

scholarly journals Identification of Botrytis cinerea Genes Up-Regulated During Infection and Controlled by the Gα Subunit BCG1 Using Suppression Subtractive Hybridization (SSH)

2004 ◽  
Vol 17 (5) ◽  
pp. 537-546 ◽  
Author(s):  
Christian Schulze Gronover ◽  
Corinna Schorn ◽  
Bettina Tudzynski
Keyword(s):  
Botrytis Cinerea ◽  
Differentially Expressed Genes ◽  
Suppression Subtractive Hybridization ◽  
Target Genes ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Wild Type ◽  
In Planta ◽  
Cell Wall Degrading Enzymes ◽  
Fungal Genes

The Gα subunit BCG1 plays an important role during the infection of host plants by Botrytis cinerea. Δbcg1 Mutants are able to conidiate, penetrate host leaves, and produce small primary lesions. However, in contrast to the wild type, the mutants completely stop invasion of plant tissue at this stage; secondary lesions have never been observed. Suppression subtractive hybridization (SSH) was used to identify fungal genes whose expression on the host plant is specifically affected in bcg1 mutants. Among the 22 differentially expressed genes, we found those which were predicted to encode proteases, enzymes involved in secondary metabolism, and others encoding cell wall-degrading enzymes. All these genes are highly expressed during infection in the wild type but not in the mutant. However, the genes are expressed in both the wild type and the mutant under certain conditions in vitro. Most of the BCG1-controlled genes are still expressed in adenylate cyclase (bac) mutants in planta, suggesting that BCG1 is involved in at least one additional signaling cascade in addition to the cAMP-depending pathway. In a second SSH approach, 1,500 clones were screened for those that are specifically induced by the wild type during the infection of bean leaves. Of the 22 BCG1-controlled genes, 11 also were found in the in planta SSH library. Therefore, SSH technology can be successfully applied to identify target genes of signaling pathways and differentially expressed genes in planta.

Profiling of differentially expressed genes in ectomycorrhizal fungus Pisolithus tinctorius responding to mycorrhiza helper Brevibacillus reuszeri MPt17

Biologia ◽  
2014 ◽  
Vol 69 (4) ◽  
Author(s):  
Ai-Dong Zhou ◽  
Xiao-Qin Wu ◽  
Lan Shen ◽  
Xu-Ling Xu ◽  
Lin Huang ◽  
...  
Keyword(s):  
Ectomycorrhizal Fungus ◽  
Pisolithus Tinctorius ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Fungal Mycelium ◽  
Functional Categories ◽  
Protein Sequence Database ◽  
Suppression Subtraction Hybridization ◽  
Subtraction Hybridization ◽  
Total Rna

AbstractA cDNA library of the ectomycorrhizal (ECM) fungus Pisolithus tinctorius Pt2 after interaction with the mycorrhiza helper bacterium (MHB) Brevibacillus reuszeri MPt17 was constructed by suppression subtraction hybridization. Total RNA from B. reuszeri MPt17 exudates treated Pi. tinctorius Pt2 was used as a “tester” and total RNA from nonbacterial treated Pi. tinctorius Pt2 was used as a “driver.” Among the differentially expressed sequences, a BLASTX in the NCBI non-redundant protein sequence database revealed that 75% of the non-redundant sequences (147 out of 196) were highly similar to known proteins (E-value < e−5). Twelve sequences were annotated as mycelium development function combining with a potential functional categories using gene ontology. Quantitative real-time PCR analysis showed that all of the 3 symbiosis regulated acidic polypeptide genes were all up-regulated in the MPt17-treated Pt2. These results provide evidence that the MHB B. reuszeri MPt17 could significantly change the expression of symbiosis-related genes and genes in mycelium development in ECM fungus, and also support the hypothesis that the MHB functions as helper though promotion on fungal mycelium.

scholarly journals Analysis of small RNA silencing in Zymoseptoria tritici – wheat interactions

2018 ◽  
Author(s):  
Graeme J. Kettles ◽  
Bernhard J. Hofinger ◽  
Pingsha Hu ◽  
Carlos Bayon ◽  
Jason J. Rudd ◽  
...  
Keyword(s):  
Small Rna ◽  
Rna Virus ◽  
Control Measure ◽  
Pathogenic Fungi ◽  
Fungal Colonization ◽  
In Planta ◽  
Zymoseptoria Tritici ◽  
Mrna Targets ◽  
Fungal Genes

AbstractCross-kingdom small RNA (sRNA) silencing has recently emerged as a mechanism facilitating fungal colonization and disease development. Here we characterized RNAi pathways in Zymoseptoria tritici, a major fungal pathogen of wheat, and assessed their contribution to pathogenesis. Computational analysis of fungal sRNA and host mRNA sequencing datasets was used to define the global sRNA populations in Z. tritici and predict their mRNA targets in wheat. 389 in planta-induced sRNA loci were identified. sRNAs generated from some of these loci were predicted to target wheat mRNAs including those potentially involved in pathogen defense. However, molecular approaches failed to validate targeting of selected wheat mRNAs by fungal sRNAs. Mutant strains of Z. tritici carrying deletions of genes encoding key components of RNAi such as Dicer-like (DCL) and Argounate (AGO) proteins were generated, and virulence bioassays suggested that these are dispensable for full infection of wheat. Nonetheless, our results did suggest the existence of non-canonical DCL-independent pathway(s) for sRNA biogenesis in Z. tritici. dsRNA targeting essential fungal genes applied in vitro or generated from an RNA virus vector in planta in a procedure known as HIGS (Host-Induced Gene Silencing) was ineffective in preventing Z. tritici growth or disease. We also demonstrated that Z. tritici is incapable of dsRNA uptake. Collectively, our data suggest that RNAi approaches for gene function analyses in this fungal species and potentially also as a control measure may not be as effective as has been demonstrated for some other plant pathogenic fungi.

scholarly journals Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Neetu Goyal ◽  
Garima Bhatia ◽  
Naina Garewal ◽  
Anuradha Upadhyay ◽  
Kashmir Singh
Keyword(s):  
Vitis Vinifera ◽  
Downy Mildew ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Differential Expression Analysis ◽  
Gene Families ◽  
Pathogen Resistance ◽  
Differentially Expressed ◽  
Phylogenetic Study ◽  
In Planta

Abstract Background Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes. Results In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions. Conclusion The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes.

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