Transcriptomic responses of the biocontrol yeast Pichia anomala to aflatoxigenic Aspergillus flavus

Abstract: Pichia anomala (Wickerhamomyces anomalus) WRL-076 is a biocontrol yeast which has been shown to inhibit growth and aflatoxin production of Aspergillus flavus. The molecular mechanism of biological control was further characterized by the temporal transcriptome response of P. anomala to A. flavus in a liquid growth medium. Total RNA was extracted and processed using an Illumina TruSeq RNA Sample Prep kit. RNA-seq reads were mapped to the W. anomalus genome using tophat2 with default settings. Differential expression analysis was performed using edgeR. Gene ontology (GO) annotation of P. anomala was retrieved from http://genome.jgi.doe.gov/. Enrichment of GO categories in differentially regulated genes was determined using Fisher’s exact test in the R environment. In comparison of yeast gene expression with and without A. flavus, a large number of genes were differentially expressed. At 24 h, 662 genes and 679 genes out of a total of 6423 genes were up- and down-regulated respectively, specifically genes involved in protein phosphorylation, protein kinase, DNA-templated regulation of transcription, and microtubule-based movement. They were enriched in the down-regulated genes at 24 h, but in up-regulation at later time points. This suggests that P. anomala was recuperating from the competition of A. flavus. Transport was enriched in up-regulated genes at 48 h, which implies that P. anomala was actively utilizing nutrients from the environment to build its biocontrol activities.