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Background  The filamentous fungus  Trichoderma reesei , the most widely used cellulase producer, also has promising applications in lignocellulose-based biorefinery: consolidated bioprocessing for the production of high value-added products. However, such applications are thwarted by the time-consuming metabolic engineering processes (design–build–test–learn cycle) for  T. reesei , resulted from (i) the spore separation-mediated purification as the multinucleate hyphae, (ii) transformant screening for high expression levels since unavailable of episomal expression system, and (iii) cases of inexpressible heterologous proteins.    Results  In this study, a GFP-fusion coupled fluorescence-activated cell sorting (FACS) platform was established to speed up the build and test process of the DBTL cycle, by enabling rapid selection for expressible heterologous genes and bypassing both laborious spore separation and transformant screening. Here, the feasibility of flow cytometry in analyzing and sorting  T. reesei  cells harboring GFP-fused expressible protein was proven, as well as the application of the platform for constitutive promoter strength evaluation. As a proof-of-concept, the platform was employed to construct the first  T. reesei  strain producing fatty alcohol, resulting in up to 2 mg hexadecanol being produced per gram biomass. Pathway construction was enabled through rapid selection of functional fatty acyl-CoA reductase encoding gene  Tafar1  from three candidate genes and strains with high expression level from spore pools. As a result of using this method, the total costed time for the build and test cycle using  T. reesei,  subsequently, reduced by approx. 75% from 2 months to 2 weeks.    Conclusion  This study established the GFP-fusion coupling FACS platform and the first filamentous fungal fatty alcohol-producing cell factory, and demonstrated versatile applications of the platform in the metabolic engineering of filamentous fungi, which can be harnessed to potentially advance the application of filamentous fungi in lignocellulose-based biorefinery.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1223-8) contains supplementary material, which is available to authorized users.

A GFP-fusion coupling FACS platform for advancing the metabolic engineering of filamentous fungi