Anthocyanins produce different-colored pigments in plant organs, which provide ornamental value. Thus, this study was conducted to understand the mechanism of anthocyanin synthesis in ornamental plants. Phoebe bournei, a Chinese specialty tree, has high ornamental and economic value due to its rich leaf color and diverse metabolic products. Here, the metabolic data and gene expression of red P. bournei leaves at the three developmental stages were evaluated to elucidate the color-production mechanism in the red-leaved P. bournei species. First, metabolomic analysis identified 34 anthocyanin metabolites showing high levels of cyanidin-3-O-glucoside (cya-3-O-glu) in the S1 stage, which may suggest that it is a characteristic metabolite associated with the red coloration of the leaves. Second, transcriptome analysis showed that 94 structural genes were involved in anthocyanin biosynthesis, especially flavanone 3′-hydroxy-lase (PbF3′H), and were significantly correlated with the cya-3-O-glu level. Third, K-means clustering analysis and phylogenetic analyses identified PbbHLH1 and PbbHLH2, which shared the same expression pattern as most structural genes, indicating that these two PbbHLH genes may be regulators of anthocyanin biosynthesis in P. bournei. Finally, overexpression of PbbHLH1 and PbbHLH2 in Nicotiana tabacum leaves triggered anthocyanin accumulation. These findings provide a basis for cultivating P. bournei varieties that have high ornamental value.

WUSCHEL-related homeobox (WOX) transcription factor (TF)-encoding genes play crucial roles during embryo development. The function of WOX genes in embryonic development has been thoroughly studied in Arabidopsis thaliana, but little is known about their function in woody species, especially Phoebe bournei, an endemic and endangered species in China. In the present study, a total of 15 WOX genes were identified in P. bournei, and phylogenetic analysis resulted in their assignment to three typical clades: an ancient clade, an intermediate clade, and a modern/WUS clade. The gene structure and sequence characteristics and the physicochemical properties of WOX proteins were also analyzed. Promoter prediction indicated that WOX genes are likely involved in plant growth and development and hormone responses. Subsequently, we evaluated the expression patterns of WOX genes in response to auxin (IAA), abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. According to tissue-specific expression patterns, we screened nine WOX genes that were present in embryonic calli and that might participate in the somatic embryogenesis (SE) of P. bournei. Furthermore, the expression profiles of these nine WOX genes during three phases of embryogenic calli development and three phases of somatic embryo development, namely, spheroid embryogenesis, immature cotyledon-producing embryogenesis and mature cotyledon-producing embryogenesis, were monitored. Overall, we systematically analyzed the expression patterns of WOX genes in P. bournei during SE, the information of which provides a basis for further elucidating the molecular mechanism through which WOX TFs function in P. bournei embryo development.

Calmodulin (CaM) and calmodulin-like (CML) proteins are major Ca²⁺ sensors involved in the regulation of plant development and stress responses by converting Ca²⁺ signals into appropriate cellular responses. However, characterization and expression analyses of CaM/CML genes in the precious species, Phoebe bournei, remain limited. In this study, five PbCaM and sixty PbCML genes were identified that only had EF-hand motifs with no other functional domains. The phylogenetic tree was clustered into 11 subgroups, including a unique clade of PbCaMs. The PbCaMs were intron-rich with four EF-hand motifs, whereas PbCMLs had two to four EF-hands and were mostly intronless. PbCaMs/CMLs were unevenly distributed across the 12 chromosomes of P. bournei and underwent purifying selection. Fragment duplication was the main driving force for the evolution of the PbCaM/CML gene family. Cis-acting element analysis indicated that PbCaMs/CMLs might be related to hormones, growth and development, and stress response. Expression analysis showed that PbCaMs were generally highly expressed in five different tissues and under drought stress, whereas PbCMLs showed specific expression patterns. The expression levels of 11 candidate PbCaMs/CMLs were responsive to ABA and MeJA, suggesting that these genes might act through multiple signaling pathways. The overexpression of PbCaM3/CML13 genes significantly increased the tolerance of yeast cells to drought stress. The identification and characterization of the CaM/CML gene family in P. bournei laid the foundation for future functional studies of these genes.

Bamboo is one of the most important non-timber forest resources worldwide. It has considerable economic value and unique flowering characteristics. The long juvenile phase in bamboo and unpredictable flowering time limit breeding and genetic improvement and seriously affect the productivity and application of bamboo forests. Members of SQUA-like subfamily genes play an essential role in controlling flowering time and floral organ identity. A comprehensive study was conducted to explain the functions of five SQUA-like subfamily genes in Phyllostachys edulis. Expression analysis revealed that all PeSQUAs have higher transcript levels in the reproductive period than in the juvenile phase. However, PeSQUAs showed divergent expression patterns during inflorescence development. The protein–protein interaction (PPI) patterns among PeSQUAs and other MADS-box members were analyzed by yeast two-hybrid (Y2H) experiments. Consistent with amino acid sequence similarity and phylogenetic analysis, the PPI patterns clustered into two groups. PeMADS2, 13, and 41 interacted with multiple PeMADS proteins, whereas PeMADS3 and 28 hardly interacted with other proteins. Based on our results, PeSQUA might possess different functions by forming protein complexes with other MADS-box proteins at different flowering stages. Furthermore, we chose PeMADS2 for functional analysis. Ectopic expression of PeMADS2 in Arabidopsis and rice caused early flowering, and abnormal phenotype was observed in transgenic Arabidopsis lines. RNA-seq analysis indicated that PeMADS2 integrated multiple pathways regulating floral transition to trigger early flowering time in rice. This function might be due to the interaction between PeMADS2 and homologous in rice. Therefore, we concluded that the five SQUA-like genes showed functional conservation and divergence based on sequence differences and were involved in floral transitions by forming protein complexes in P. edulis. The MADS-box protein complex model obtained in the current study will provide crucial insights into the molecular mechanisms of bamboo’s unique flowering characteristics.

Mixed-species plantations are proven to enhance phosphorus (P) availability in subtropical forest ecosystems. However, the effect of coniferous-broadleaf mixed plantations on soil P cycling dynamics remains poorly understood. Through a long-term field experiment, the study investigated how mixed plantations influence soil P fractions, phoD and pqqC genes, and associated bacterial communities in bulk and rhizosphere soils. Results showed that compared to monocultures, the introduction of broad-leaved trees significantly increased labile P pools, particularly in the rhizosphere. Amplicon-based community profiling of phoD/pqqC genes demonstrated distinct compositional shifts in P-solubilizing bacterial communities across forest types and soil compartments. The pqqC-harboring bacterial communities were more closely related to the P fractions. More importantly, plant properties were important in explaining bulk soil labile P responses, while in rhizosphere soil, labile P was more strongly associated with soil properties, positively affecting labile P. These findings elucidate the complex interplay between tree diversity, microbial functional traits, and soil P transformations. This study underscores the critical role of mixed plantations in promoting microbial-mediated P mobilization and provides valuable insights for designing sustainable forest management strategies to optimize P utilization in subtropical ecosystems.

Phoebe chekiangensis is an indigenous, endangered, and valuable timber and garden tree species in China, which is notable for having a short juvenile phase (early flowering), unique among the Phoebe genus. However, the molecular mechanisms regulating the flowering of P. chekiangensis remain unexplored, primarily due to the lack of transcriptomic or genomic data. In the present study, transcriptome sequencing yielded 53 million RNA reads, resulting in 111,250 unigenes after de novo assembly. Of these, 47,525 unigenes (42.72%) were successfully annotated in the non-redundant (Nr) database. Furthermore, 15,605 unigenes were assigned to Clusters of Orthologous Groups (KOGs), and 36,370 unigenes were classified into Gene Ontology (GO) categories. A total of 16,135 unigenes were mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, involving 298 pathways. Based on the expression levels, Gibberellin signaling pathway-related genes were the most predominant expression levels. Hormonal analysis showed that gibberellin (GA) levels varied across tissues and flowering stages, as GA20 levels in leaves were low during full bloom, while GA1 and GA5 levels peaked in flowers. Furthermore, several key genes involved in gibberellin biosynthesis, including CPS, GID1, GA20ox, GA3ox, and GA2ox, exhibited stage-specific expression patterns. Certain genes were highly expressed during the initial phases of flowering, while others, like GA3ox and GA2ox, reached peak expression at full bloom. These findings provide valuable insights into the molecular mechanisms underlying flowering in P. chekiangensis, laying the foundation for future breeding efforts. This transcriptome dataset will serve as an important public resource for molecular research on this species, facilitating the discovery of functional genes related to its growth, development, and flowering regulation.