A Tale of Two Molds: Comparative Penicillium spp. transcriptomics reveals conserved pathways, processes, and loci associated with ungerminated conidia and blue mold decay

A transcriptomic approach was implemented using two Penicillium species to identify genes related to fungal aggressiveness in apple fruit and loci contained in ungerminated conidia. Total RNA was isolated from ungerminated conidia and decayed apple fruit infected with P. expansum R19 (aggressive) or P. polonicum RS1 (weak). There were 2,442 differentially expressed genes (DEGs) between the R19 and RS1 in apple and comparisons within species between apple and conidia revealed 4,404 DEGs for R19, and 2935 for RS1, respectively. Gene ontology (GO) revealed differential regulation in fungal transport and metabolism genes expressed during decay, suggesting a flux in nutrient acquisition and detoxification strategies. In R19, the oxidoreductase GO category comprised 20% of all groups differentially expressed in decayed apple verses ungerminated conidia in addition to those involved in hydrogen peroxide metabolism. Ungerminated conidia from both species showed higher expression of genes encoding the glyoxylate shunt and beta-oxidation, specifying the earliest metabolic requirements for germination Overall design: Four replicate samples of highly agressive Penicillium expansum R19 from the decayed margin of apple fruit, four replicate samples of R19 ungerminated conidia, four replicate samples from weakly virulent P. polonicum RS1 from apple tissue, and four replicate samples of RS1 ungerminated conidia all were used to extract RNA for RNA-Seq to compare transcriptomes of the two blue mold pathogens before infecting apple and during apple infection. Transcripts were quality filtered and assembled before finding log2 fold change expression differences between the four sample types. Data was visualized for interpretation via heat maps of virulence genes of interest, volcano plots of all genes, and venn diagrams of differentially regulated genes. Gene ontology and Kegg mapping were used to group genes based on molecular function and pathway shifts between the pathways shifts between pathogen type and pre or post infection status. Both strains were also evaluated for germination timing (14 hours postinoculation and 24 hpi - 3 technical replicates/trial, two trials), radial growth on PDA media (3, 5, and 7 days postinoculation - 3 technical replicates/trial, two replicate trials), and lesion size on infected apples (10 apples/inoculum/trial, two trials) over time to demonstrate differences between growth and pathogenicity of the strains.