show Abstracthide AbstractThe leaves and roots of I.indigodica. are used in the traditional Chinese medicine of Daqingye and Banlangen, which have a variety of pharmacological activities including antibacterial, anti-inflammatory and antiviral. In Chinese medicine, the medicinal effects of I. indigotica. are thought to be reflected in its cold property, and some studies suggest that plants with cold property need more energy in strong light to maintain growth due to their low energy metabolism levels. Mitochondria are the main site of energy metabolism, and miRNAs are involved in plant growth and development as endogenous non-coding factors, but whether they affect plant energy metabolism by regulating the structure and function of mitochondria has rarely been reported. The results showed that in I. indigotica., the structural integrity of mitochondria was positively correlated with light intensity, and contents of ATP and AMP, NADH, CCR, CCO and ATP synthase activity was positively correlated with light intensity (P<0.05); 12 miRNA-mRNA pairs were identified to be associated with mitochondria (P<0.05), and a mechanistic map was deduced for the involvement of miRNAs in the regulation of mitochondrial biological processes. Combined with RT-qPCR validation, it was concluded that ath-miR167a-5p positively regulated LETM1 to affect mitochondrial structure, bra-miR400-5p and bna-MIR169m-p3_1ss15CT negatively regulated GRXS15 and CMC4, respectively, thus affecting SDH and CCO activities, and miR395a - APS4 might be related to the utilization of ATP and sulfate assimilation. In summary, the structural integrity and energy metabolism of mitochondria were positively correlated with light intensity, and miRNAs affected plant energy metabolism by regulating mitochondrial structure and function. The results of this study provide guidance for cultivation and quality control of I. indigotica., while complementing and enriching the molecular mechanisms of light effects on mitochondria.