Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Genes for the production of a broad range of fungal secondary metabolites are frequently colinear. The prevalence of such gene clusters was systematically examined across the genome of the cereal pathogen Fusarium graminearum. The topological structure of transcriptional networks was also examined to investigate control mechanisms for mycotoxin biosynthesis and other processes. RESULTS: The genes associated with transcriptional processes were identified, and the genomic location of transcription-associated proteins (TAPs) analyzed in conjunction with the locations of genes exhibiting similar expression patterns. Highly conserved TAPs reside in regions of chromosomes with very low or no recombination, contrasting with putative regulator genes. Co-expression group profiles were used to define positionally clustered genes and a number of members of these clusters encode proteins participating in secondary metabolism. Gene expression profiles suggest there is an abundance of condition-specific transcriptional regulation. Analysis of the promoter regions of co-expressed genes showed enrichment for conserved DNA-sequence motifs. Potential global transcription factors recognising these motifs contain distinct sets of DNA-binding domains (DBDs) from those present in local regulators. CONCLUSIONS: Proteins associated with basal transcriptional functions are encoded by genes enriched in regions of the genome with low recombination. Systematic searches revealed dispersed and compact clusters of co-expressed genes, often containing a transcription factor, and typically containing genes involved in biosynthetic pathways. Transcriptional networks exhibit a layered structure in which the position in the hierarchy of a regulator is closely linked to the DBD structural class

27th Fungal Genetics Conference

Program and abstracts from the 27th Fungal Genetics Conference Asilomar, March 12-17, 2013

Characterisation of transcriptional elements regulating virulence during Parastagonospora nodorum infection of wheat

Recent advances have facilitated the identification of important virulence factors produced by the what pathogen Parastagonospora nodorum. Among these are necrotrophic effectors, but little is known regarding how they are regulated. This thesis presents the characterisation of important regulatory elements underpinning the disease that includes transcription factors and necrotrophic effector gene promoters

27th Fungal Genetics Conference

Program and abstracts from the 27th Fungal Genetics Conference Asilomar, March 12-17, 2013

28th Fungal Genetics Conference

Full abstracts from the 28th Fungal Genetics Conference Asilomar, March 17-22, 2015

Program and abstracts from the 24th Fungal Genetics Conference

Abstracts of the plenary and poster sessions from the 24th Fungal Genetics Conference, March 20-25, 2007, Pacific Grove, CA

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

Background Fusarium graminearum (Fg), a major fungal pathogen of cultivated cereals, is responsible for billions of dollars in agriculture losses. There is a growing interest in understanding the transcriptional regulation of this organism, especially the regulation of genes underlying its pathogenicity. The generation of whole genome sequence assemblies for Fg and three closely related Fusarium species provides a unique opportunity for such a study. Results Applying comparative genomics approaches, we developed a computational pipeline to systematically discover evolutionarily conserved regulatory motifs in the promoter, downstream and the intronic regions of Fg genes, based on the multiple alignments of sequenced Fusarium genomes. Using this method, we discovered 73 candidate regulatory motifs in the promoter regions. Nearly 30% of these motifs are highly enriched in promoter regions of Fg genes that are associated with a specific functional category. Through comparison to Saccharomyces cerevisiae (Sc) and Schizosaccharomyces pombe (Sp), we observed conservation of transcription factors (TFs), their binding sites and the target genes regulated by these TFs related to pathways known to respond to stress conditions or phosphate metabolism. In addition, this study revealed 69 and 39 conserved motifs in the downstream regions and the intronic regions, respectively, of Fg genes. The top intronic motif is the splice donor site. For the downstream regions, we noticed an intriguing absence of the mammalian and Sc poly-adenylation signals among the list of conserved motifs. Conclusion 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 reveals their functional significance, and provides new insights in their evolutionary importance among Ascomycete fungi

26th Fungal Genetics Conference at Asilomar

Program and abstracts from the 26th Fungal Genetics Conference, March 15-20, 2011

Understanding germination and pathogenicity in zygomycota species through genomic and transcriptomic approaches

Mucorales spores are the causative agents of the emerging disease mucormycosis. Mucorales species are also responsible for high quantities of food spoilage annually. The mechanism by which Mucorales spores cause disease and rot relies upon spore germination, however the mechanism underlying germination in these species remains poorly understood. Presented here are results which characterise Mucorales spore germination, through phenotypic and transcriptional studies (RNA-Seq), which followed the defined germination phenotype throughout. Hallmark pathways are identified through analysis of differentially expressed genes and co-transcriptional networks, providing targets for germination inhibition. With the resulting transcriptional data, the genome of Rhizopus delemar was enriched and analysed, thus providing better information on the Mucoralean genome. Comparative genomics was also employed to better understand genotypic variation between Mucorales species. To examine the differences in pathogenicity between species, and assess the impact of germination stage on pathogenicity, the transcriptional profile (RNA-Seq) of selected Mucorales species was examined upon phagocytosis by innate immune cells. To better understand the corresponding host response, the transcriptional response (single cell RNA-Seq) of innate immune cells to Mucorales infection was also examined. Finally, germination targets identified through the described analyses were targeted with suspected inhibitors to confirm function in germination regulation. This work has furthered our basic understanding of germination in these ancient fungi, indicated pathways essential to the germination programme of Mucorales species, and demonstrated a crucial role played by many of these pathways in host-fungal interactions of the Mucorales

Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum.

Abstract Background: Fusarium oxysporum is one of the most common fungal pathogens causing soybean root rot and seedling blight in U.S.A. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. Results: We used RNA-seq analysis to investigate the molecular aspects of the interactions of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 h post inoculation (hpi). Markedly different gene expression profiles were observed in response to the two isolates. A peak of highly differentially expressed genes (HDEGs) was triggered at 72 hpi in soybean roots and the number of HDEGs was about eight times higher in response to the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 HDEGs, respectively). Furthermore, the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of defense-related genes, transcription factors, and genes involved in ethylene biosynthesis, secondary and sugar metabolism. Conclusions: The obtained data provide an important insight into the transcriptional responses of soybean-F. oxysporum interactions and illustrate the more drastic changes in the host transcriptome in response to the pathogenic isolate. These results may be useful in the developing new methods of broadening resistance of soybean to F. oxysporum, including the over-expression of key soybean genes