K-means clustering of differentially expressed genes identified as CAZymes (summarized in Table 3).

<p>K-means clustering of differentially expressed genes identified as CAZymes (summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone-0088689-t003" target="_blank">Table 3</a>).</p

Contig sequences classified according to their putative hydrolytic activity.

<p>Contig sequences classified according to their putative hydrolytic activity.</p

Metabolic pathways expressed in different libraries.

<p>The classification of the contigs according to the NCBI NR and KEGG databases <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone.0088689-Kanehisa2" target="_blank">[46]</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone.0088689-Kanehisa1" target="_blank">[28]</a> indicates which metabolic pathway is active under a specific culture condition.</p

Expression profiles of selected glycosyl hydrolase genes determined by RT-qPCR.

<p>The squalene-epoxidase gene was used as endogenous control. The differences between groups were considered significant at P<0.05 (Student's t test) and are indicated by *.</p

Encoded genes related to cellulose and hemicellulose depolymerization.

<p>Genes classified in the transcriptome analysis of <i>T. harzianum</i> fermentation on sugarcane bagasse.</p

The identified genes (summarized in Table 3) were resolved into three clusters.

<p>The identified genes were further classified into one of three response profiles based on where they were most highly expressed: (A) in the DSB library, (B) in the CEL library or (C) in the LAC library.</p

Molecular functions, biological process distribution and cellular localization of the transcriptome assembly.

<p>Contigs were assigned putative classifications based on homology and evaluated for their predicted involvement in molecular functions (A), biological processes (B) and cellular localization (C).</p

Results of next-generation sequencing, trimming analysis, <i>de novo</i> assembly and mapping.

<p>The raw reads were <i>de novo</i> assembled to generate contigs for further analysis and annotation.</p

Classification of sequences present in upregulated groups, according to the CAZyme database.

<p>The sequences presenting expectation values lower than 1×10⁻³, and the best alignment scores are summarized. The clusters are classified according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone-0088689-g006" target="_blank">Figure 6</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone-0088689-g007" target="_blank">7</a>.</p

Identified sequences that catalyze reactions that are potentially involved in biomass degradation.

<p>The results of identification based on homology using the NCBI NR database indicate the presence of genes that are related to the depolymerization of biomass in the transcriptome.</p