Characterizing co-expression networks underpinning maize stalk rot virulence in Fusarium verticillioides through computational subnetwork module analyses

Scientific Reports
Man S KimWon-Bo Shim

Abstract

Fusarium verticillioides is recognized as an important stalk rot pathogen of maize worldwide, but our knowledge of genetic mechanisms underpinning this pathosystem is limited. Previously, we identified a striatin-like protein Fsr1 that plays an important role in stalk rot. To further characterize transcriptome networks downstream of Fsr1, we performed next-generation sequencing (NGS) to investigate relative read abundance and also to infer co-expression networks utilizing the preprocessed expression data through partial correlation. We used a probabilistic pathway activity inference strategy to identify functional subnetwork modules likely involved in virulence. Each subnetwork modules consisted of multiple correlated genes with coordinated expression patterns, but the collective activation levels were significantly different in F. verticillioides wild type versus fsr1 mutant. We also identified putative hub genes from predicted subnetworks for functional validation and network robustness studies through mutagenesis, virulence and qPCR assays. Our results suggest that these genes are important virulence genes that regulate the expression of closely correlated genes, demonstrating that these are important hubs of their respectiv...Continue Reading

References

Sep 10, 1998·Nature Structural Biology·K L NicholsonF M Hughson
Mar 17, 2001·Nature Reviews. Molecular Cell Biology·Y A Chen, R H Scheller
Jul 27, 2001·Mammalian Genome : Official Journal of the International Mammalian Genome Society·K W SeoT Watanabe
Jun 8, 2002·Fungal Genetics and Biology : FG & B·Gagan D Gupta, I Brent Heath
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
Jul 15, 2006·Molecular Plant-microbe Interactions : MPMI·Won-Bo ShimYin-Won Lee
Sep 9, 2006·Microbiology and Molecular Biology Reviews : MMBR·Sarah MacPhersonBernard Turcotte
Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xiaoning QianByung-Jun Yoon
Jul 6, 2010·Fungal Genetics and Biology : FG & B·Chih-Li WangBrian D Shaw
Jun 8, 2011·Nucleic Acids Research·Jüri ReimandJaak Vilo
Mar 2, 2012·Molecular Microbiology·Sandra BloemendalUlrich Kück
Oct 15, 2013·Trends in Cell Biology·WanJin Hong, Sima Lev

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Datasets Mentioned

BETA
GSE108365

Methods Mentioned

BETA
gene knockout
phosphotransferase
PCR
Profiler

Software Mentioned

Image J

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