Comparative transcriptomics analyses of fruiting body development in Fusarium species

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) has been reported as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. This cosmopolitan species has also been reported as an opportunistic human pathogen, from infected soybean cyst nematodes, deer dung, and soil, and it possesses a highly active CO2 fixation mechanism. To better understand the metabolic potential of this fungus, we sequenced the genome of one isolate of F. neocosmosporiellum and compared its gene content with previously published Fusarium genomes. The predicted gene numbers were similar to F. graminearum, but the F. neocosmosporiellum genome contained more carbohydrate metabolism-related and transmembrane transport genes, and it appears to have a greater ability to utilize resources in the environment as a cosmopolitan saprotroph. Transcriptome data during perithecium development was compared with that of the model plant pathogen F. graminearum. The F. neocosmosporiellum genome included both MAT1-1 and MAT1-2 idiomorphs, as in the homothallic F. graminearum, however MAT gene organization and their expression patterns during perithecium development differed in these species. We also found that many transmembrane transport genes were differentially expressed during perithecium development, which may account for the larger perithecia of F. neocosmosporiellum. Finally, comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during perithecium development. Deletion of a novel polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype. In summary, comparative analysis of the transcriptional programs during perithecium development has provided novel insights into morphological and physiological diversification in F. neocosmosporiellum. Overall design: Time-series mRNA profiles during the perithecial development for the Fusarium neocosmosporiellum strain NRRL_22166 were generated by deep sequencing, in triplicate, using the Illumina HiSeq 2500 system.