Comparative analysis of 87,000 expressed sequence tags from the fumonisin-producing fungus Fusarium verticillioides

Abstract

Fusarium verticillioides (teleomorph Gibberella moniliformis) is a pathogen of maize worldwide and produces fumonisins, a family of mycotoxins that have been associated with several animal diseases as well as cancer in humans. In this study, we sought to identify fungal genes that affect fumonisin production and/or the plant-fungal interaction. We generated over 87,000 expressed sequence tags from nine different cDNA libraries that correspond to 11,119 unique sequences and are estimated to represent 80% of the genomic complement of genes. A comparative analysis of the libraries showed that all 15 genes in the fumonisin gene cluster were differentially expressed. In addition, nine candidate fumonisin regulatory genes and a number of genes that may play a role in plant-fungal interaction were identified. Analysis of over 700 FUM gene transcripts from five different libraries provided evidence for transcripts with unspliced introns and spliced introns with alternative 3' splice sites. The abundance of the alternative splice forms and the frequency with which they were found for genes involved in the biosynthesis of a single family of metabolites as well as their differential expression suggest they may have a biological function. Finally, analysis of an EST that aligns to genomic sequence between FUM12 and FUM13 provided evidence for a previously unidentified gene (FUM20) in the FUM gene cluster.

Cross-Species Hybridization with Fusarium verticillioides Microarrays Reveals New Insights into Fusarium fujikuroi Nitrogen Regulation and the Role of AreA and NMR

“…The development and initial characterization of an F. verticillioides Roche NimbleGen Systems, Inc. (Madison, WI) 24-mer oligonucleotide microarray comprising 16,500 probe sets have been described previously (R. Butchko and D. Brown, personal communication). Each probe set included up to 12 perfectly matching oligonucleotide probes and was designed based on an F. verticillioides EST library consisting of over 87,000 ESTs (5). Analysis of a recent annotation of F. verticillioides genomic sequence data indicates that the microarray represents over 9,300 genes (4).…”

Identification of a splicing coactivator gene that affects the production of ochratoxin a in Aspergillus carbonarius

“…A typical example is four Fusarium verticillioides genes that are located outside the fumonisin gene cluster but affect fumonisin biosynthesis (Shim and Woloshuk, 2001;Flaherty et al, 2003;Flaherty and Woloshuk, 2004;Bluhm and Woloshuk, 2006). (Brown et al, 2005), and the gene FUM21 which has a Zn(II) 2 Cys 6 DNA-binding motif, supposedly involved in the transcriptional regulation of the genes in the fumonisin cluster . The differential expression of the ASFs of FUM genes suggests that splicing regulation can play a role in fumonisin biosynthesis (Brown et al, 2005).…”

“…(Brown et al, 2005), and the gene FUM21 which has a Zn(II) 2 Cys 6 DNA-binding motif, supposedly involved in the transcriptional regulation of the genes in the fumonisin cluster . The differential expression of the ASFs of FUM genes suggests that splicing regulation can play a role in fumonisin biosynthesis (Brown et al, 2005). Some proteins that participate in the splicing mechanism show serine-and argenine-rich domains, known as RS domains.…”

Identification of a cis-acting factor modulating the transcription of FUM1, a key fumonisin-biosynthetic gene in the fungal maize pathogen Fusarium verticillioides

“…FUM20 was excluded from the analysis since its function is unknown and the gene shares no significant similarity with any previously described gene in the NCBI database, although it was proven to be transcribed ( Brown et al, 2005). Sequences were downloaded from the Broad Institute for all fungi (http://www.broadinstitute.org/scientific-community/data) with the exception of sequences of the A.niger strain ATCC1015 ( Andersen et al, 2011), which were obtained from the JGI database (http://genome.jgi-psf.org/Aspni1/Aspni1.home.html), and of the upstream sequence of the FUM1-like from C.heterostrophus ( Kroken et al, 2003), from the JGI database (http://genomeportal.jgi-psf.org/CocheC5_3/CocheC5_3.home.html).…”