Abstract:Monascus spp. are important industrial microorganisms that can produce beneficial metabolites such as monascus pigments（MPs），moncolin K（MK），and gamma-aminobutyric acid（GABA）. The genomic analysis was carried out for the global regulatory factor genes VeA and VelB of four Monascus strains（M7，NRRL 1597，NRRL 1596，and YY-1）with high production of red pigment. The results showed that the proteins encoded by VeA in the four strains contained a velvet domain，a nuclear localization signal（NLS），and a proline-，glutamic acid-，serine-，and threonine-rich（PEST）sequence.The protein encoded by VelB contained two velvet domains but lacked an NLS region. The similarity of VeA and VelB sequences between Monascus and typical filamentous fungi was within the ranges of 37.4%-62.5% and 51.2%-84.1%，respectively. This suggested that VeA and VelB in Monascus had similar functions to those in other filamentous fungi. The primary structures of Monascus VeA and VelB were mainly composed of proline and serine，with no obvious transmembrane structure or signal peptide. Monascus VeA was mainly located in the nucleus，while VelB existed in both the nucleus and cytoplasm.Both proteins had multiple serine，threonine，and tyrosine kinase phosphorylation sites. The secondary structure of Monascus VeA was mainly composed of beta-sheets and random coils，while that of Monascus VelB was mainly composed of alpha-helices，beta-sheets，and random coils. The threedimensional structures of VeA and VelB in Monascus were similar to those in typical filamentous fungi. The protein-protein interaction network showcased that VeA and VelB interacted with each other. The results suggested that the functions and mechanisms of VeA and VelB in Monascus were similar to those in other fungi，and the two proteins might be involved in regulating the growth，development，and secondary metabolism of strains.