Supplemental Material for Cary et al., 2018
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Supplemental Figure 1 -Volcano plot of log2 folder change vs. log10 P-value of all
the genes in ∆ℎ𝑏𝑥1 versus ∆ℎ𝑏𝑥1-com (top row) and control versus ∆ℎ𝑏𝑥1-com (bottom row)
at the 6 h, 24 h, and 48 h time points. DEGs are pink dots, other genes are green dots.
Pink dots with positive log2 fold change values are up-regulated DEGs. Pink dots with negative
log2 fold change values are down-regulated DEGs. The x-axis represents the log2 of the fold
change as determined by limma. The y-axis is the log10 of the adjusted p value from limma. The
cut off fold change value to determine differential expression is greater than 2 or less than 0.5.
The cut off adjusted p value to determine differential expression was greater than 0.05.
Supplemental Figure 2 - GO terms associated with DEGs in ∆hbx1 versus Control at 6 h, 24 h, and 48 h. The minus log10 of the p-value of DEGs in each term is proportional to the length of the bars. GO annotations and p-value as determined by FungiDB(http://fungidb.org/fungidb/): (i) biological processes is shown in red, (ii) cellular components in blue, and (iii) molecular functions in green. Down regulated genes are to the left of the origin and up regulated to the right.
Supplemental Figure 3 – Heat map of average RPKM values of genes on a log scale found in secondary metabolite gene clusters of interest. The average RPKM value was found by averaging all the RPKM values of all replicates corresponding to that treatment at three different time points: 6 h, 24 h, 48 h.
Table S1- Differentially expressed gene analysis of hbx1 transcriptome. Analysis of differentially expressed genes reported as log fold change. Analysis was done between each strain at all time points. Corresponding p-value between comparisons to determine significance are included.
Table S2- List of selected hbx1-dependent developmental genes. A list of transcription factor genes was obtained from Krijgsheld et al. (2015) and compared to the list of DEGs looking for hbx1 dependent genes. Expression values are those between the wild type (WT) and Δhbx1 at all time points.
Table S3- Full list of hbx1-dependent transcription factors. A list of transcription factor genes obtained from the Fungal Transcription Factor Database and compared to the list of DEGs looking for those that are hbx1 -dependent. Expression values are those between the wild type (WT) and Δhbx1 at all time points.
Table S4- hbx1-dependent putative virulence factors. Differentially expressed hbx1 genes were compared to the dataset of genes differentially expressed during corn infection, from Dolezal et al. (2013). Genes were categorized in different groups: those virulence-related genes showing upregulation were compared to hbx1 DEGs (both up or down regulated), and virulence-related genes that showed downregulation were also compared to hbx1 DEGs (both up or down regulated). Expression values are those between the wild type (WT) and Δhbx1.
Table S5- hbx1-dependent secretory genes possibly involved in virulence. A focused subset of Table S4 showing secretory genes possibly associated with virulence that are differentially expressed in the absence of hbx1. Data was obtained from Table S4 and applied to the FunSecKB2 database to select secretome genes that were either curated or “highly likely secreted”. Genes were then categorized in groups: those secretory genes showing upregulation were compared to hbx1 DEGs (both up or down regulated), and secretory genes that showed downregulation were also compared to hbx1 DEGs (both up or down regulated). Expression values are those between the wild type (WT) and Δhbx1.