Global transcriptional profiling of Ustilago bromivora during axenic growth and pathogenic development

To provide insights into expression patterns of the genes encoding putatively secreted proteins in U. bromivora during saprophytic growth and in planta, we conducted RNA-seq analyses. To this end, we isolated RNA from axenic U. bromivora UB1 culture and from stems of twelve day old B. hybridum Bd28 plants that were spore-inoculated with U. bromivora. Among the 6756 transcripts found to be expressed in our dataset, 493 were significantly upregulated in planta compared to axenic culture (logFC > 2, adjusted p-value < 0.1), while 1138 transcripts were significantly downregulated. Notably, transcripts predicted to encode secreted proteins are significantly enriched among the upregulated transcripts compared to all annotated genes. Overall design: RNA-seq analysis of axenically grown Ustilago bromivora UB1 and Brachypodium hybridum Bd28 infected with Ustilago bromivora spores (twelve days after planting of infected caryopses) using Illumina NGS. The study was performed in triplicates.