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Title: Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes

item KUMAR, LOKESH - Broad Institute Of Mit/harvard
item BREAKSPEAR, ANDREW - University Of Minnesota
item Kistler, Harold
item MA, LI-JUN - Broad Institute Of Mit/harvard
item XIE, XIAOHUI - University Of California

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2010
Publication Date: 3/26/2010
Citation: Kumar, L., Breakspear, A., Kistler, H.C., Ma, L., Xie, X. 2010. Systematic Discovery of Regulatory Motifs in Fusarium graminearum by Comparing Four Fusarium Genomes. Genome Biology. 11(208):1-13.

Interpretive Summary: Fusarium graminearum (Fg), a major pathogen of cultivated cereals, is responsible for billions of dollars in agricultural losses. There is a growing interest in understanding the mechanisms by which genes in this harmful pathogen are turned on and off, especially if this regulation controls the ability of the fungi to cause disease or to allow toxins to contaminate food. The genome sequencing of Fg and three closely related Fusarium species provided a unique opportunity to understand the regulation of genes. Applying comparative genomics approach, we developed a computational process to systematically discover evolutionarily conserved portions of the genes that control when and where they are expressed. Factors which regulate gene expression of important traits potentially could be exploited for disease control measures. These disease management strategies may involve disruption of vital fungal developmental pathways. The primary users of the research in this publication will be other scientists engaged in research to improve disease management on small grain crops.

Technical Abstract: Using comparative genomics, we discovered 73 candidate regulatory motifs in the promoter regions of four Fusarium species. Nearly 30% of them are highly enriched in the promoter region of Fg genes that are specifically associated with a functional category. Through the comparison to Saccharomyces cerevisiae (Sc) and Schizosaccharomyces pombe (Sp), we observed the conservation of TFs, their binding sites and the target genes regulated by these TFs related to pathways known to respond under stress conditions or phosphate metabolism. In addition, this study also revealed 69 and 39 conserved motifs in the downstream regions and the intronic regions respectively. The top intronic motifs include the splice donor and acceptor sites. For the downstream regions, we noticed an intriguing absence of the mammalian and Sc poly-adenylation signals among the list of conserved motifs. This study provides the first comprehensive list of candidate regulatory motifs in Fg, and underscores the power of comparative genomics in revealing functional elements among related genomes. The conservation of regulatory pathways among the Fusarium genomes and the two yeast species suggests their functional significance, and provides new insights in their evolutionary implications among Ascomycete fungi.