AbstractBackgroundA major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce enzymes that can saccarify lignocellulose and cocktails from several fungi, including well-studied species such asTrichoderma reeseiandAspergillus niger, are available commercially for this process. Such commercially-available enzyme cocktails are not necessarily representative of the array of enzymes used by the fungi themselves when faced with a complex lignocellulosic material. The global induction of genes in response to exposure ofT. reeseito wheat straw was explored using RNA-seq and compared to published RNA-seq data and model of howA. nigersenses and responds to wheat straw.ResultsInT. reesei, levels of transcript that encode known and predicted cell-wall degrading enzymes were very high after 24 h exposure to straw (approximately 13% of the total mRNA) but were less than recorded inA. niger(approximately 19% of the total mRNA). Closer analysis revealed that enzymes from the same glycoside hydrolase families but different carbohydrate esterase and polysaccharide lyase families were up-regulated in both organisms. Accessory proteins which have been hypothesised to possibly have a role in enhancing carbohydrate deconstruction inA. nigerwere also uncovered inT. reeseiand categories of enzymes induced were in general similar to those inA. niger. Similarly toA. niger, antisense transcripts are present inT. reeseiand their expression is regulated by the growth condition.ConclusionsT. reeseiuses a similar array of enzymes, for the deconstruction of a solid lignocellulosic substrate, toA. niger. This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi. This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate. The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation byT. reeseiand provide information which could prove useful for efficient production of second generation biofuels.