Integrated metabolomics, PacBio SMRT, and Illumina sequencing analyses provide insights into molecular profiles associated with radial trunk growth in Chinese fir (Cunninghamia lanceolata)

) is a coniferous timber species endemic to China, widely used in furniture manufacturing and construction industries. Metabolite transport and conversion within tree trunk tissues play a crucial role in radial growth. Current research on metabolite changes between the phloem and xylem of tree trunks remains scarce. Owing to the lack of whole-genome sequence information for Chinese fir, studies on the molecular mechanisms underlying its key traits have progressed slowly. This study employed an integrated approach combining metabolomics, PacBio SMRT and illumina sequencing analyze metabolites and transcripts in four distinct regions of Chinese fir: phloem, outer sapwood, inner sapwood, and the transition zone. A total of 398 metabolites were identified in the trunk tissues of Chinese fir. The phloem was found to be primarily enriched in primary metabolites, such as amino acids, sugars, and organic acids, In contrast, the xylem not only accumulated primary metabolites but also exhibited significant enrichment of secondary metabolites including polyphenols, hormones, and pharmacologically active compounds. Among secondary metabolites, the highest number of differentially expressed metabolites were enriched in the phenylpropanoid biosynthesis pathway. Coniferin-a key precursor in lignin biosynthesis, exhibited the highest accumulation among the detected phenolic compounds across all four regions. Among KEGG pathways related to amino acid metabolism, the Arginine and proline metabolism pathway had the highest enrichment of differential metabolites. Metabolites such as glutamate, ornithine, and 4-aminobutanoate in this pathway showed the highest content in the phloem, with a gradual decrease from the phloem to the transition zone. Genes belonging to transcription factor families such as WRKY, bHLH, HB-HD-ZIP, and AP2 were identified, suggesting that these genes may be involved in regulating be involved in regulating xylem formation in Chinese fir. This study provides a foundational molecular profile of metabolic activities in the trunk tissues of Chinese fir and offers valuable information for future research on the molecular mechanisms underlying radial trunk growth in forest trees.