Loblolly pine (Pinus taeda L.) is an important tree for afforestation with substantial economic and ecological value. Many metabolites with pharmacological activities are present in the tissues of P. taeda. However, the biosynthesis regulatory mechanisms of these metabolites are poorly understood. In the present study, transcriptome and metabolome analyses were performed on five tissues of P. taeda. A total of 40.4 million clean reads were obtained and assembled into 108,663 unigenes. These were compared with five databases, revealing 39,576 annotated unigenes. A total of 13,491 differentially expressed genes (DEGs) were observed in 10 comparison groups. Of these, 487 unigenes exhibited significantly different expressions in specific tissues of P. taeda. The DEGs were explored using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis. We identified 343 and 173 candidate unigenes related to the biosynthesis of terpenoids and flavonoids, respectively. These included 62 R2R3-MYB, 30 MYB, 15 WRKY, seven bHLH, seven ERF, six ZIP, five AP2, and one WD40 genes that acted as regulators in flavonoid and/or terpenoid biosynthesis. Additionally, metabolomics analysis detected 528 metabolites, among which 168 were flavonoids. A total of 493 differentially accumulated metabolites (DAMs) were obtained in 10 comparison groups. The 3,7-Di-O-methyl quercetin was differentially accumulated in all the comparison groups. The combined transcriptome and metabolome analyses revealed 219 DEGs that were significantly correlated with 45 DAMs. Our study provides valuable genomic and metabolome information for understanding P. taeda at the molecular level, providing a foundation for the further development of P. taeda-related pharmaceutical industry.

Pinaceae is the largest family of conifers, dominating forest ecosystems and serving as the backbone of northern, temperate and mountain forests. The terpenoid metabolism of conifers is responsive to pests, diseases, and environmental stress. Determining the phylogeny and evolution of terpene synthase genes in Pinaceae may shed light on early adaptive evolution. We used different inference methods and datasets to reconstruct the Pinaceae phylogeny based on our assembled transcriptomes. We identified the final species tree of Pinaceae by comparing and summarizing different phylogenetic trees. The genes encoding terpene synthase (TPS) and cytochrome P450 proteins in Pinaceae showed a trend of expansion compared with those in Cycas. Gene family analysis revealed that the number of TPS genes decreased while the number of P450 genes increased in loblolly pine. Expression profiles showed that TPSs and P450s were mainly expressed in leaf buds and needles, which may be the result of long-term evolution to protect these two vulnerable tissues. Our research provides insights into the phylogeny and evolution of terpene synthase genes in Pinaceae and offers some useful references for the investigation of terpenoids in conifers.

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

Introduction: Pine wilt disease (PWD) is a highly destructive infectious disease that severely damages pine forests worldwide. Because symptoms emerge first in the tree crown, detection from unmanned aerial vehicles (UAVs) is efficient. However, most methods perform only binary classification and lack pixel-level staging, which leads to missed initial symptoms and confusion with other species. Methods: We propose MSCF-LUNet, a lightweight three-stage semantic segmentation model based on multi-scale context fusion. The model uses an improved multi-scale patch embedding guided by attention with relative position encoding (AWRP) to adapt the sampling field of view and to fuse local details with global context. Under contextual attention, the network learns fine-grained features and location cues. Results: In complex environments, MSCF-LUNet achieves 89.56% precision, 92.13% recall, 88.92% intersection over union (IoU), and 96.54% pixel accuracy (PA), balancing performance and computational cost. Discussion: The model effectively segments PWD-infected regions and determines disease stages from remote-sensing imagery.

Agarwood is a kind of important and precious traditional Chinese medicine. With the decreasing of natural agarwood, artificial cultivation has become more and more important in recent years. Quantifying the formation of agarwood is an essential work which could provide information for guiding cultivation and controlling quality. But people only can judge the amount of agarwood qualitatively by experience before. Fluorescence multispectral imaging method is presented to measure the agarwood quantitatively in this paper. A spectral cube from 450 nm to 800 nm was captured under the 365 nm excitation sources. The nonagarwood, agarwood, and rotten wood in the same sample were distinguished based on analyzing the spectral cube. Then the area ratio of agarwood to the whole sample was worked out, which is the quantitative information of agarwood area percentage. To our knowledge, this is the first time that the formation of agarwood was quantified accurately and nondestructively.

Chloroplasts are utilized in genetic studies due to their compact genomes and simple structure. While their inheritance is predominantly maternal in most plants, it is paternal in many gymnosperms. This study investigated intraspecific variation and inheritance patterns of the chloroplast genome in loblolly pine ( Pinus taeda ). We sequenced chloroplast DNA from 54 individuals in the second generation core breeding population and performed genome-wide SNP discovery via a custom Python pipeline. From the 81 initially identified SNP loci, a final set of 32 high-frequency loci (variation frequency > 5%) was selected for validation, comprising 14 in intergenic spacer regions and 18 within gene regions. Despite overall conservation, we identified a hypervariable region in the ycf1 gene, which contained 8 SNP loci and accounted for 44.4% of all coding region SNPs. We then designed 23 primer pairs to amplify the regions containing these candidate variants across a 9 × 5 tester design, encompassing a total of 75 individuals (45 progeny and 30 parents). Phylogenetic and haplotype analyses based on these SNPs revealed no maternal haplotype sharing between any of the eight maternal parents and their progeny, and showed that progeny consistently clustered with specific paternal parents, such as W03 and N4. Furthermore, analysis of SNP profiles allowed reconstruction of paternal lineages and detection of patterns indicative of pollen contamination. Collectively, these results validate both the paternal inheritance of the chloroplast genome in P. taeda and the potential utility of chloroplast markers in conifer breeding.