biostudies-literatureSun XCAAS | Agricultural Science and Technology Innovation ProgramChina Agricultural Research System (CARS) of MOF and MARAMOST | National Key Research and Development Program of China (NKPs)MOST | National Natural Science Foundation of China (NSFC)MOST | National Key Research and Development Program of ChinaCAAS | Agricultural Science and Technology Innovation Program (ASTIP)China Postdoctoral Science FoundationMOST | National Natural Science Foundation of ChinaChina Postdoctoral Science Foundation (China Postdoctoral Foundation Project)e0208223https://www.ebi.ac.uk/biostudies/studies/S-EPMC11267940biostudies-literatureUnknown90(7)Genetic engineering at the genomic scale provides a rapid means to evolve microbes for desirable traits. However, in many filamentous fungi, such trials are daunted by low transformation efficiency. Differentially expressed genes under certain conditions may contain important regulatory factors. Accordingly, although manipulating these subsets of genes only can largely reduce the time and labor, engineering at such a sub-genomic level may also be able to improve the microbial performance. Herein, first using the industrially important cellulase-producing filamentous fungus <i>Trichoderma reesei</i> as a model organism, we constructed suppression subtractive hybridization (SSH) libraries enriched with differentially expressed genes under cellulase induction (MM-Avicel) and cellulase repressApplied and environmental microbiologySub-genomic RNAi-assisted strain evolution of filamentous fungi for enhanced protein production.PMC11267940BX20220347, 2022M7234482021YFC210020432302785CAAS-ZDRW202305CARS-41Tu THuang HYao BZhao TLuo HSun XGao FYang SSu XFan CfalseSub-genomic RNAi-assisted strain evolution of filamentous fungi for enhanced protein production.Genetic engineering at the genomic scale provides a rapid means to evolve microbes for desirable traits. However, in many filamentous fungi, such trials are daunted by low transformation efficiency. Differentially expressed genes under certain conditions may contain important regulatory factors. Accordingly, although manipulating these subsets of genes only can largely reduce the time and labor, engineering at such a sub-genomic level may also be able to improve the microbial performance. Herein, first using the industrially important cellulase-producing filamentous fungus <i>Trichoderma reesei</i> as a model organism, we constructed suppression subtractive hybridization (SSH) libraries enriched with differentially expressed genes under cellulase induction (MM-Avicel) and cellulase repress2024-01-01T00:00:00Z2024 Jul2025-04-18T14:21:39.279Z2025-04-04T21:45:16.889ZS-EPMC112679403889988610.1128/aem.02082-23