Tilia amurensis Rupr. is a crucial species widely used in our life, because its wood is easy to process due to its low specific gravity and good elasticity. To understand the effect of the latitudinal gradients on T. amurensis metabolites profiles, we collected data from six different latitudes about physiological indicators such as temperature, light, and precipitation, then analyzed the differences in T. amurensis metabolite profiles from these different latitudes. The metabolomes of the six latitudes (SFS 49°28′53.26″ N, WY 48°06′51.314″ N, LS 47°11′1.71″ N, BL 45°7′55″ N, BH 43°50′16.8″ N, and TS 40′30.89″ N) were compared using GC–MS/LC–MS, and significant differences in primary and secondary metabolites were found. A total of 29 primary metabolites were screened by orthogonal partial least squares discriminant analysis (OPLS-DA), and 34 flavonoids were determined using the targeted metabolomics methods. A total of 11 flavonoids in secondary metabolites were significantly different in the LS region compared with other areas. The main physiological indicator that differs between the LS region and other regions was the annual sunshine percentage. This indicates that the metabolic differences in T. amurensis at different latitudes may be affected by environmental factors such as annual sunshine percentage. As a vital species, T. amurensis metabolites change with different environmental factors, indicating that this species has different adaptability to the environment of different latitudes.
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