Abstract
The epidemic of stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), would reduce wheat (Triticum aestivum) yields seriously. Traditional experimental methods are difficult to discover the interaction between wheat and Pst. Multi-omics data analysis provides a new idea for efficiently mining the interactions between host and pathogen. We used 140 wheat-Pst RNA-Seq data to screen for differentially expressed genes (DEGs) between low susceptibility and high susceptibility samples, and carried out Gene Ontology (GO) enrichment analysis. Based on this, we constructed a gene co-expression network, identified the core genes and interacted gene pairs from the conservative modules. Finally, we checked the distribution of Nucleotide-binding and leucine-rich repeat (NLR) genes in the co-expression network and drew the wheat NLR gene co-expression network. In order to provide accessible information for related researchers, we built a web-based visualization platform to display the data. Based on the analysis, we found that resistance-related genes such as TaPR1, TaWRKY18 and HSP70 were highly expressed in the network. They were likely to be involved in the biological processes of Pst infecting wheat. This study can assist scholars in conducting studies on the pathogenesis and help to advance the investigation of wheat-Pst interaction patterns.
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Abbreviations
- Pst:
-
Puccinia Striiformis F. sp. tritici
- DEGs:
-
Differentially expressed genes
- GO:
-
Gene ontology
- NLR:
-
Nucleotide-binding and leucine-rich repeat
- HSPs:
-
Heat shock proteins
- Yr:
-
Yellow rust
- PAMPS:
-
Pathogen-associated molecular patterns
- PTI:
-
PAMPs triggered immunity
- ETI:
-
Effector triggered immunity
- PRRs:
-
Pattern recognition receptors
- WGCNA:
-
Weighted gene co-expression network analysis
- L2FC:
-
Log2foldchange
- GS:
-
GeneSignificant
- MM:
-
ModuleMembership
- TNL:
-
Toll/interleukin-1 receptor-nucleotide binding site-leucine rich repeat
- CNL:
-
Coiled-coil-nucleotide binding site-leucine rich repeat
- RNL:
-
Resistance to powdery mildew8-nucleotide binding site-leucine rich repeat
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Funding
This project was supported by the Research Program for Network Security and Information of the Chinese Academy of Sciences (CAS-WX2021SF-0109) and Research on Key Technologies for Identification and Inspection of Tobacco Raw Materials and Cigarette-like Products Based on DNA Molecular Markers of Yunnan Branch of China National Tobacco Corporation (2023530000241027).
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Y.W., Q.L. and K.Z. conceived and designed the experiments. Y.W., D.C., K.L. analyzed the RNA-Seq data. Y.W., W.C. built the webpage. Y.W. wrote the manuscript. Q.L., F.H. and Z.T. supervised the research and edited the manuscript. All authors have read and agreed to the submitted version of the manuscript.
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Wang, Y., Zhang, K., Chen, D. et al. Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici. Arch Microbiol 206, 241 (2024). https://doi.org/10.1007/s00203-024-03925-5
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DOI: https://doi.org/10.1007/s00203-024-03925-5