Filamentous fungi are essential ecosystem members and major platforms for industrial biomanufacturing, where their morphological differentiation strongly influences broth rheology, mass/oxygen transfer, secretion efficiency, stress tolerance, and ultimately productivity. However, the intricate network in which process-specific cues are sensed and integrated to reprogram the endogenous developmental pathways remains incompletely understood, limiting rational morphology engineering of the industrial filamentous fungi. This review summarizes recent advances in the regulation of morphological differentiation of filamentous fungi, integrating internal and external signaling along with molecular control of spore germination, polarity establishment, hyphal extension/branching, and cell wall-plasma membrane homeostasis. We discuss how distinct morphologies affect performance in submerged and solid-state fermentation, and we overview the practical control strategies including inoculation design, environmental and hydrodynamic optimization, microparticle-enhanced cultivation, and genetic reprogramming. Finally, we highlight emerging monitoring approaches and recent progress in machine learning and modeling within AI-enabled biomanufacturing, proposing an integrated gene–morphology–function–titer perspective for next-generation fungal cell factories.

Base editors are regarded as reliable and precise editing tools due to their ability to efficiently and accurately modify the target genes without inducing double-strand breaks (DSBs). Notably, base editors offer distinct advantages in base editing, particularly in multiplex gene editing. However, application of base editors in the filamentous fungus Trichoderma remains underdeveloped. In this study, two cytosine base editors (CBE), designated as rAPOBEC1-CBE and mini-SDD7-CBE, respectively, were constructed in Trichoderma koningiopsis. Three targets related with cellulase production were chosen for testing editing efficiency of these two systems. The mini-SDD7-CBE system exhibited a maximum editing efficiency of 80%, with the editing window predominantly situated at positions 16 to 20 upstream of the PAM sequence in T. koningiopsis. Utilizing the mini-SDD7-CBE system, simultaneous editing of two and three genes was successfully executed. The overall editing efficiency was primarily influenced by the lowest editing efficiency of an individual single guide RNA (sgRNA). This study provides a convenient tool for the precise genome engineering of Trichoderma, thereby facilitating the extensive application of base editing techniques in filamentous fungi.