| Summary: | <i>Mikania micrantha</i> is one of the worst invasive species globally and can cause significant negative impacts on agricultural and forestry economics, particularly in Asia and the Pacific region. The rust <i>Puccinia spegazzinii</i> has been used successfully as a biological control agent in several countries to help manage <i>M. micrantha</i>. However, the response mechanisms of <i>M. micrantha</i> to <i>P. spegazzinii</i> infection have never been studied. To investigate the response of <i>M. micrantha</i> to infection by <i>P. spegazzinii</i>, an integrated analysis of metabolomics and transcriptomics was performed. The levels of 74 metabolites, including organic acids, amino acids, and secondary metabolites in <i>M. micrantha</i> infected with <i>P. spegazzinii</i>, were significantly different compared to those in plants that were not infected. After <i>P. spegazzinii</i> infection, the expression of the TCA cycle gene was significantly induced to participate in energy biosynthesis and produce more ATP. The content of most amino acids, such as L-isoleucine, L-tryptophan and L-citrulline, increased. In addition, phytoalexins, such as maackiain, nobiletin, vasicin, arachidonic acid, and JA-Ile, accumulated in <i>M. micrantha</i>. A total of 4978 differentially expressed genes were identified in <i>M. micrantha</i> infected by <i>P. spegazzinii</i>. Many key genes of <i>M. micrantha</i> in the PTI (pattern-triggered immunity) and ETI (effector-triggered immunity) pathways showed significantly higher expression under <i>P. spegazzinii</i> infection. Through these reactions, <i>M. micrantha</i> is able to resist the infection of <i>P. spegazzinii</i> and maintain its growth. These results are helpful for us to understand the changes in metabolites and gene expression in <i>M. micrantha</i> after being infected by <i>P. spegazzinii</i>. Our results can provide a theoretical basis for weakening the defense response of <i>M. micrantha</i> to <i>P. spegazzinii</i>, and for <i>P. spegazzinii</i> as a long-term biological control agent of <i>M. micrantha</i>.
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