Nanmu (Phoebe zhennan) is an extremely valuable tree plant that is the main source of famous “golden-thread nanmu” wood. The potential metabolites and gene regulation mechanisms involved in golden thread formation are poorly understood, even though the color change from sapwood to heartwood has been investigated in several tree plants. Here, five radial tissues from sapwood to heartwood were compared via integrative metabolomic and transcriptomic analysis to reveal the secondary metabolites and molecular mechanisms involved in golden thread formation. During heartwood formation, gradual starch grain loss is accompanied by the cell lumen deposition of lipids and color-related extractives. Extractives of 20 phenylpropanoids accumulated in heartwood, including cinnamic acids and derivatives, coumarin acid derivatives, and flavonoids, which were identified as being closely related to the golden thread. Phenylpropanoids co-occurring with abundant accumulated metabolites of prenol lipids, fatty acyls, steroids, and steroid derivatives may greatly contribute to the characteristics of golden thread formation. Additionally, the expression of nine genes whose products catalyze phenylpropanoid and flavonoids biosynthesis was upregulated in the transition zone, then accumulated and used to color the heartwood. The expression levels of transcription factors (e.g., MYB, bHLH, and WRKY) that act as the major regulatory factors in the synthesis and deposition of phenylpropanoid and flavonoids responsible for golden thread formation were also higher than in sapwood. Our results not only explain golden thread formation in nanmu, but also broaden current knowledge of special wood color formation mechanisms. This work provides a framework for future research focused on improving wood color.

Walnut oil is a high-value oil product. Investigation of the variation and the main climatic factors affecting the oil’s chemical composition is vital for breeding and oil quality improvement. Therefore, the fatty acid, micronutrients, and secondary metabolites compositions and contents in walnut oil were determined in three species: Juglans regia L. (common walnut), J. sigillata Dode (iron walnut), and their hybrids (Juglans sigillata Dode × J. regia L.), which were cultivated aat different sites. The major fatty acids were linoleic (51.39–63.12%), oleic (18.40–33.56%), and linolenic acid (6.52–11.69%). High variation in the contents of fatty acids, micronutrients, and secondary metabolites was found between both species and sites. Interestingly, myristic, margaric, and margaroleic acid were only detected in the hybrids’ walnut oil, yet α-tocopherol was only detected in common and iron walnut oil. Climatic factors significantly affected the composition and content of fatty acid, whereas δ-tocopherol was mostly dependent on the genetic factors. The average relative humidity explained the most variation in the fatty acids, micronutrients, and secondary metabolites, which showed a significant positive and negative effect on the monounsaturated fatty acids and polyunsaturated fatty acids, respectively. These findings contribute to the provision of better guidance in matching sites with walnut trees, and improvement of the nutritional value of walnut oil.