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Background  The filamentous fungus  Penicillium oxalicum  is a potential alternative to  Trichoderma reesei  for industrial production of a complete cellulolytic enzyme system for a bio-refinery. Comparative omics approaches can support rational genetic engineering and/or breeding of filamentous fungi with improved cellulase production capacity. In this study, comparative genomic, transcriptomic and secretomic profiling of  P. oxalicum  HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106 were employed to screen for novel regulators of cellulase and xylanase gene expression.    Results  The 30.62 Mb  P .  oxalicum  HP7-1 genome was sequenced, and 9834 protein-coding genes were annotated. Re-sequencing of the mutant EU2106 genome identified 274 single nucleotide variations and 12 insertion/deletions. Comparative genomic, transcriptomic and secretomic profiling of HP7-1 and EU2106 revealed four candidate regulators of cellulase and xylanase gene expression. Deletion of these candidate genes and measurement of the enzymatic activity of the resultant mutants confirmed the identity of three regulatory genes.  POX02484  and  POX08522 , encoding a putative Zn(II) 2 Cys 6  DNA-binding domain and forkhead protein, respectively, were found to be novel, while PoxClrB is an ortholog of ClrB, a key transcriptional regulator of cellulolytic enzyme gene expression in filamentous fungi. Δ POX02484  and Δ POX08522  mutants exhibited significantly reduced β-glucosidase activity, increased carboxymethylcellulose cellulase and xylanase activities, and altered transcription level of cellulase and xylanase genes compared with the parent strain Δ PoxKu70 , with Avicel as the sole carbon source.    Conclusions  Two novel genes,  POX02484  and  POX08522 , were found and characterized to regulate the expression of cellulase and xylanase genes in  P. oxalicum . These findings are important for engineering filamentous fungi to improve cellulase and xylanase production.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-016-0616-9) contains supplementary material, which is available to authorized users.

biotechnology for biofuels

Comparative genomic, transcriptomic and secretomic profiling of Penicillium oxalicum HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106, and identification of two novel regulatory genes of cellulase and xylanase gene expression