ARS | Publication request: Fusarium genomics: Polyketide synthases and mRNA alternative splicing

Submitted to: Multicrop Aflatoxin and Fumonisin Elimination and Fungal Genomics Workshop-The Peanut Foundation
Publication Type: Abstract
Publication Acceptance Date: October 24, 2007
Publication Date: October 24, 2007
Citation: Brown, D.W., Butchko, R.A., Proctor, R. 2007. Fusarium genomics: Polyketide synthases and mRNA alternative splicing [abstract]. Multicrop Aflatoxin/Elimination and Fungal Genetics Workshop. p. 38.

Technical Abstract: Genomic technologies have greatly expanded the pool of fungal-related data in recent years. A significant challenge to researchers examining plant pathogenesis and mycotoxin biosynthesis is to efficiently mine this data to identify structural and regulatory genes, and general regulatory mechanisms involved in these processes. We reasoned that a comparison of all of the polyketide synthases (PKSs) present in four Fusarium genomes (F. verticillioides, F. graminearum, F. oxysporum sequenced by the Broad Institute, and F. solani sequenced by the Joint Genome Institute) may identify specific PKSs required for pathogen growth and/or for primary metabolism. Basic Local Alignment Tool analysis led to the identification of 58 PKSs, many of which have been examined previously to some degree. Phylogenetic analysis of the PKSs and analysis of predicted domains identified will be discussed. A number of years ago, we examined over 720 F. verticillioides fumonisin gene expressed sequence tags (ESTs) and found that eight of 17 FUM genes had message ribonucleic acid species that differed in the pattern of processed introns. Based on the number of alternative splice (AS) events and their accumulation late in culture, we suggested that the AS forms play a role in fumonisin synthesis. In order to better understand alternative splicing in F. verticillioides, we searched the entire EST data base (87,000 ESTs) and identified 354 genes with AS events which correspond to approximately 4% of the represented genes. Of the AS events in coding regions, 261 (76%) are retention events, 22% have alternative borders, and 2% skip an exon(s). This is significantly different than observed in humans or plants where intron retention events are around 10% and 56% respectively while exon skip events are around 58% and 8% respectively. A significant portion of the F. verticillioides AS transcripts could generate proteins with an altered amino acid sequence leading to multiple possible functional proteins from the same gene.