The filamentus fungus Neurospora crassa possess strong ability of lignocellulosic biomass degradation in nature,and thus it has been used as a suitable model for studying gene transcriptional regulatory and protein secretory mechanisms of fungal lignocellulosic enzymes.When producing enzymes,the unfolded protein response (UPR) play a critical role in coordinating gene expression,nascent peptide folding and mature protein sorting of client lignocellulase.Using high-throughput RNA-Seq method,we sought to decipher the UPR mechanism in N.crassa under cellulase induction condition so as to facilitate the development of hyper-secretion fungal cell factory.We determined the differences and patterns of the transcriptional profiles of wildtype strain FGSC 2489 as it treated with two different UPR inducing drugs dithiothreitol (DTT) and tunicamycin (TM).Gene differencial expression analysis indicated that at least 134 genes were remarkably up-regulated in both conditions which function throughout the secretory pathway including protein folding,translocation,protein glycosylation,vesicular transport,ER-associated degradation and apoptosis.Genes of most extracellular secretory protein were significantly down-regulated in DTT treatment condition and less extent under TM treatment condition were also observed.We then detected the alternative splicing events using denovo tanscriptome assembly and genomic mapping and alignment program,approximately 350 novel splicing sites were identified when compared to published data.Finally,we intensive analyzed the knock-out mutants of transcription factors and kinase genes to identify novel components of the UPR pathway,potential candidates are currently being validated.RNAseq-based transcriptome analysis of the unfolded protein response in the lignocellulolytic fungus Neurospora crassa