e *cre1* gene in *T. reesei* SP4, QM9414 and RUT-C30 using the primer pair creF/creR. A 2.9-kb length fragment was amplified from QM9414 and SP4 but not from RUT-C30. **d** PCR analysis of the full-length *cre1* gene in *T. reesei* SP4, QM9414 and RUT-C30 using the primer pair creF/creRUTr. The primers provided a 1.9-kb fragment corresponding to the truncated *cre1* gene from RUT-C30, but yielded a larger fragment (4.4 kb) from QM9414 and SP4. **Additional file 2: Figure S2.** PCR and phenotypic analysis of the Δ*cre1* strain *T. reesei* SDC11. **a** PCR analysis of *T. reesei* SDC11 with SP4 as control. 1 and 2 represent the fragment (upstream region and open reading frame of gene *cre1*) amplificated by the prime pair cre1-2426UF/cre1-1069R in *T. reesei* SDC11 and SP4, respectively; 3 and 4 represent the internal fragment of gene *cre1* amplificated by the prime pair cre1-497F/cre1-1069R in *T. reesei* SDC11 and SP4, respectively. 5 and 6 represent the fragment of gene *pyrG* amplificated by the prime pair pyrG-UF1/pyrG-2426DR in *T. reesei* SDC11 and SCP11, respectively. **b** Southern blot analysis of the genomic DNA isolated from SP4 and SCP11, which were digested with *Eco*RI/*Hin*dIII. A 5.5-kb fragment is present in the parental strain SP4, and a 7.0-kb band is shown in Δ*cre1* + *pyrG* strain SCP11. **c** Growth of *T. reesei* SN1, Δ*cre1* + *pyrG* strain SCP11 and Δ*cre1* strain SDC11 on MM plate. **d** Growth of *T. reesei* SP4, Δ*cre1* + *pyrG* strain SCP11 and Δ*cre1* strain SDC11 on the MM plate containing uracil (0.1%). **Additional file 3: Figure S3.** Renaturing SDS-PAGE assay of BGL activities from the fermentation broths of *T. reesei* SDC11 and SP4 with equal FPA loading (0.04 FPA). **Additional file 4: Figure S4.** PCR and phenotypic analysis of the *bglA* overexpression strain *T. reesei* SCB18. **a** Graphical representation of the *bglA* overexpression cassette. **b** PCR analysis of the *T. reesei* SCB18 and SDC11 strains. 1 and 3 represent the chimeric fragments spanning th