Fig. 1

Cellulose-induced transcription factors in P. funiculosum NCIM1228 and ∆Mig1 identified by RNA-seq. a RNA-seq experimental design to conduct transcriptomic analysis of NCIM1228 and ∆Mig1 grown in Mandel's medium with 4% glucose (MM glucose) and 4% cellulase (MM cellulose) for 72 h. b Volcano plot of differentially expressed genes in cellulose with respect to glucose in NCIM1228 and ∆Mig1. Venn diagram showing the commonly upregulated genes between NCIM1228 and ∆Mig1. c Venn diagram of common and exclusive transcription factors (TFs) upregulated in NCIM1228 and ∆Mig1; 8 of the common TFs showed a higher log2-fold change in NCIM1228 than in ∆Mig1, whereas 6 of them showed equivalent or higher expression in ∆Mig1. d Hierarchical (left) clustering of normalized FPKM abundance (log₂) of 41 TFs in NCIM1228 and ∆Mig1 grown on glucose and cellulose. Three transcription factors related to biomass degradation were identified: Clr-2 (TF for cellulase) and Ctf1a and Ctf1b (TFs for cutinase). e Transcript counts of ctf1a, clr-2, and ctf1b in NCIM1228 and ∆Mig1 grown in glucose and cellulose. Statistical significance was determined by a one-tailed, unequal variance t test. f Quantitative RT‒PCR of selected TFs in NCIM1228 and ∆Mig1 grown in MM glucose and MM cellulose for 72 h. The C(T) value in cellulose was normalized to that in glucose