Multi-Omics Analysis Reveals the Resistance Mechanism and the Pathogens Causing Root Rot of .

is a traditional Chinese medicinal herb used for more than 2,000 years. Root rot in can cause brown discoloration (necrosis) in the fibrous roots and rhizomes, leading to plants wilting and dying. However, little information exists about the resistance mechanism and the potential pathogens of the root rot of plants. As a result, in order to investigate the relationship between the underlying molecular processes and the pathogenesis of root rot, transcriptome and microbiome analyses were performed on healthy and diseased rhizomes. This study found that root rot can lead to the significant reduction of medicinal components of Coptis, including thaliotrine, columbamine, epiberberin, coptisine, palmatine chloride, and berberine, affecting its efficacy quality. In the present study, , Fusarium , and Fusarium solani were identified as the main pathogens causing root rot in . At the same time, the genes in phenylpropanoid biosynthesis, plant hormone signal transduction, plant-pathogen interaction, and alkaloid synthesis pathways were involved in the regulation of root rot resistance and medicinal component synthesis. In addition, harmful pathogens (, and F. solani) also induce the expression of related genes in root tissues to reduce active medicinal ingredients. These results provide insights into the root rot tolerance study and pave the way for process disease resistance breeding and quality production of . Root rot disease significantly reduces the medicinal quality of . In the present study, results found that the fibrous and taproot have different tactics in response to rot pathogen infection. , Fusarium , and Fusarium solani were isolated and identified to cause different degrees of root rot. These results are helpful for researchers to further explore the mechanism of resistance to rhizoma Coptis root rot.