Fig. 2.

Transcriptome analysis of P. anomala at low pH. The RNA-seq data from three biological replicates were analyzed and a correlation plot of the FPKM values was obtained for the replicates (a). The normalized FPKM values were calculated using the Tuxedo pipeline [18] and were used to classify the P. anomala transcriptome using a boxplot of the four gene expression classes (based on cutoff in the Additional file 4: Figure S3). The number of the genes in each class are above each boxplot (b)