Fig. 3
Comparison of RNA-Seq and real-time RT-PCR results. Expression profiles of a conidiation-specific protein 10 of Aspergillus niger (CON10), b transcription factor CPH2 of Debaryomyces hansenii (CPH2), c flagellar transcriptional regulator of Cupriavidus metallidurans (FlhD), d short-chain type dehydrogenase/reductase of Pichia stipitis (SDR), e transmembrane pair family protein of Pseudomonas protegens (TMP), f GPI-anchored protein 45 of P. stipitis (GPI-AP), g probable homoserine kinase of Schizosaccharomyces pombe (HSK), h 2,3-bisphosphoglycerate-independent phosphoglycerate mutase of A. niger (iPGAM), i meiosis upregulated gene UPF0590 Penicillium chrysogenum (MUG), j 50S ribosomal protein L14 of Azorhizobium caulinodans (RPS50), k S-adenosylmethionine synthase 1 of Saccharomyces cerevisiae (SAM1), l ß-glucosidase 4 of Fusarium oxysporum (BGL), m 30 kDa heat shock protein of D. hansenii (HSP30), n 4-hydroxy-2-oxovalerate aldolase of Trichoderma atroviride (HOA), o D-arabinitol dehydrogenase of Armillaria mellea (ArDH). Blue dotted lines represent expression levels (FPKM) calculated by RNA-Seq analysis and reported as means and standard errors of three replicates for each condition: the simplified soil microcosm collected at the beginning of the experiment (SSM0) and 24 h after incubation either without exogenous fungi (SSM), with the biocontrol agent T. atroviride (SSM+T), with the plant pathogen A. mellea (SSM+A) or with both (SSM+T+A). White histograms represent the relative expression levels calculated by quantitative real-time RT-PCR analysis as normalised relative quantities (NRQ;[52]) as compared to the mean expression level in all conditions, using Actin 1 of Schizosaccharomyces pombe and Elongation factor 1α of Fusarium oxysporum as reference genes