Carminic acid (CA) is a high-value natural anthraquinone pigment used in foods, cosmetics, textiles, and pharmaceuticals, but its current industrial supply depends largely on extraction from the scale insect Dactylopius coccus, creating constraints in yield, cost, sustainability, and allergen control. This review summarizes recent progress from pathway elucidation to microbial production. We first outline the structure, occurrence, applications, and biosynthetic logic of CA, emphasizing the convergence of type III polyketide assembly with insect-associated tailoring reactions, especially C-glycosylation. We then compare heterologous production strategies in Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Aspergillus nidulans, focusing on chassis-specific advantages, bottlenecks, precursor supply, malonyl-CoA engineering, dynamic regulation, enzyme compatibility, compartmentalization, and downstream processing. Structurally related anthraquinone pigments are further discussed to extract broader design principles for pathway diversification and synthetic biology. Finally, we highlight key challenges for industrial translation, including low titers, incomplete enzyme characterization, host–pathway incompatibility, and scalable purification, and propose integrated strategies combining precursor-pathway rewiring, AI-assisted enzyme engineering, biosensor-based regulation, and process optimization to develop competitive microbial cell factories.

Natural products remain a major source of structurally diverse and biologically active small molecules, yet traditional activity-guided discovery is labor-intensive and prone to rediscovery, while untargeted genome mining often lacks efficient prioritization criteria for biosynthetic gene clusters (BGCs). Self-resistance-gene guided discovery has emerged as a powerful strategy to address this limitation. In producing organisms, toxic metabolites are typically accompanied by genetically encoded self-protection mechanisms, such as resistant target homologs, duplicated housekeeping genes, detoxification enzymes, repair systems, or transporters. When co-localized with BGCs, these determinants serve as functional markers for predicting bioactivity and, in some cases, molecular targets prior to compound isolation. Over the past decade, this concept has evolved into a target-directed genome mining framework supported by tools and databases including ARTS, FunARTS, antiSMASH, and MIBiG. This review summarizes the biological basis, workflow, representative advances, and limitations of this strategy. Self-resistance genes can thus be viewed as functional beacons for accelerating bioactive natural product discovery.

Natural products remain a major source of structurally diverse and biologically active small molecules, yet traditional activity-guided discovery is labor-intensive and prone to rediscovery, while untargeted genome mining often lacks efficient prioritization criteria for biosynthetic gene clusters (BGCs). Self-resistance-gene guided discovery has emerged as a powerful strategy to address this limitation. In producing organisms, toxic metabolites are typically accompanied by genetically encoded self-protection mechanisms, such as resistant target homologs, duplicated housekeeping genes, detoxification enzymes, repair systems, or transporters. When co-localized with BGCs, these determinants serve as functional markers for predicting bioactivity and, in some cases, molecular targets prior to compound isolation. Over the past decade, this concept has evolved into a target-directed genome mining framework supported by tools and databases including ARTS, FunARTS, antiSMASH, and MIBiG. This review summarizes the biological basis, workflow, representative advances, and limitations of this strategy. Self-resistance genes can thus be viewed as functional beacons for accelerating bioactive natural product discovery.