Having a spiral grain is considered to be one of the most important wood properties influencing wood quality. Here, transcriptome profiles and metabolome data were analyzed in the straight grain and twist grain of Pinus yunnanensis. A total of 6644 differential expression genes were found between the straight type and the twist type. A total of 126 differentially accumulated metabolites were detected. There were 24 common differential pathways identified from the transcriptome and metabolome, and these pathways were mainly annotated in ABC transporters, arginine and proline metabolism, flavonoid biosynthesis, isoquinoline alkaloid biosynthesis, linoleic acid metabolism, phenylpropanoid, tryptophan metabolism, etc. A weighted gene coexpression network analysis showed that the lightblue4 module was significantly correlated with 2′-deoxyuridine and that transcription factors (basic leucine zipper (bZIP), homeodomain leucine zipper (HD-ZIP), basic helix–loop–helix (bHLH), p-coumarate 3-hydroxylase (C3H), and N-acetylcysteine (NAC)) play important roles in regulating 2′-deoxyuridine, which may be involved in the formation of spiral grains. Meanwhile, the signal transduction of hormones may be related to spiral grain, as previously reported. ARF7 and MKK4_5, as indoleacetic acid (IAA)- and ethylene (ET)-related receptors, may explain the contribution of plant hormones in spiral grain. This study provided useful information on spiral grain in P. yunnanensis by transcriptome and metabolome analyses and could lay the foundation for future molecular breeding.

Pinus yunnanensis Franch. is a common woodland species in the southwest of China. Its trunk frequently twists during growth, affecting timber quality. The explanation for the twisted-trunk formation is unknown. In this work, we examined the variety of endophytes and metabolites by comparing the straight and twisted trunk types of P. yunnanensis. The results showed that the twisted trunk had a distinct endosymbiont composition compared to the straight trunk. Pseudomonas and Craurococcus bacteria, as well as the fungus taxa Phaeosphaeria and Epichloë, spread significantly more in the twisted trunk compared to the straight trunk. However, there was less Dechloromonas in the twisted trunk. Metabolomic analysis revealed differences in metabolites in the straight and twisted trunks, which were associated with four metabolic pathways: beta-alanine metabolism, metabolism of Jasmonic acid and trans-Zeatin metabolism, linoleic acid metabolism, and pentose phosphate pathway. The compounds were linked to certain endophyte bacteria species. Our findings suggested that the twisted trunk was subjected to more stress than the straight trunk because of endosymbionts. Moreover, we speculated that hormone signal transduction and the absorption, transport, and utilization of phosphorus elements and their interaction with microorganisms may be closely connected to the formation of twists. This is the first study to characterize the microbiome and metabolome in the twisted trunks of P. yunnanensis, and the results enhance our understanding of the underlying causes of twisted-trunk formation in P. yunnanensis.