Supplemental Material for Cary et al., 2018
Jeffrey W. Cary
Sarah Entwistle
Timothy Satterlee
Brian M. Mack
Matthew Gilbert
Perng K. Chang
Leslie Scharfenstein
Yanbin Yin
Ana M. Calvo
10.25387/g3.7304252.v1
https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Cary_et_al_2018/7304252
<p><b>Supplemental
Figure 1 -</b>Volcano
plot of log2 folder change vs. log10 P-value of all</p>
<p>the genes in ββππ₯1 versus ββππ₯1-com (top row)
and control versus ββππ₯1-com (bottom row)</p>
<p>at the 6 h, 24 h, and 48 h time
points. DEGs are pink dots, other genes are green dots.</p>
<p>Pink dots with positive log2 fold
change values are up-regulated DEGs. Pink dots with negative</p>
<p>log2 fold change values are down-regulated
DEGs. The x-axis represents the log2 of the fold</p>
<p>change as determined by limma. The
y-axis is the log10 of the adjusted p value from limma. The</p>
<p>cut off fold change value to
determine differential expression is greater than 2 or less than 0.5.</p>
<p>The cut off adjusted p value to
determine differential expression was greater than 0.05.</p>
<p> </p>
<p><b>Supplemental
Figure 2</b>
- GO terms associated with DEGs in β<i>hbx1</i>
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.</p>
<p> </p>
<p><b>Supplemental
Figure 3 β</b>
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.</p>
<p><b> </b></p>
<p><b>Table
S1- Differentially expressed gene analysis of <i>hbx1 </i>transcriptome</b>. 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.</p>
<p> </p>
<p><b>Table
S2- List of selected <i>hbx1-</i>dependent
developmental genes</b>.
A list of transcription factor genes was obtained from Krijgsheld et al. (2015)
and compared to the list of DEGs looking for <i>hbx1 </i>dependent genes. Expression values are those between the wild
type (WT) and Ξ<i>hbx1 </i>at all time
points.</p>
<p> </p>
<p><b>Table
S3- Full list of <i>hbx1-</i>dependent
transcription factors</b>.
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 <i>hbx1 </i>-dependent. Expression values are
those between the wild type (WT) and Ξ<i>hbx1
</i>at all time points.</p>
<p> </p>
<p><b>Table
S4- <i>hbx1-</i>dependent putative virulence
factors. </b>Differentially
expressed <i>hbx1 </i>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 <i>hbx1
</i>DEGs (both up or down regulated), and virulence-related genes that showed downregulation
were also compared to <i>hbx1</i> DEGs<i> </i>(both up or down regulated). Expression
values are those between the wild type (WT) and Ξ<i>hbx1</i>.</p>
<p> </p>
<p><b>Table
S5- <i>hbx1-</i>dependent secretory genes
possibly involved in virulence. </b>A focused subset of Table S4 showing
secretory genes possibly associated with virulence that are differentially
expressed in the absence of <i>hbx1. </i>Data
was obtained from Table S4 and applied to the FunSecKB2 database to select secretome
genes that were either curated or βhighly likely secretedβ. Genes were then
categorized in groups: those secretory genes showing upregulation were compared
to <i>hbx1 </i>DEGs (both up or down
regulated), and secretory genes that showed downregulation were also compared
to <i>hbx1</i> DEGs<i> </i>(both up or down regulated). Expression values are those between
the wild type (WT) and Ξ<i>hbx1</i>.</p>
2018-11-13 17:09:41
Aspergillus flavus
Hbx1
secondary metabolism
fungal development
transcriptome
Genetics