Reconstructing the phylogeny of the pine family (Pinaceae) has historically been problematic because analyses based on morphological characters and genetic analyses using small numbers of sequences have produced incongruent results. Such discrepancies may have resulted from continuous gene flow or genome mixing events among certain pine species. Here, we reconstructed a species-level tree of the Pinaceae using genome-wide data from seven pine species. A multi-locus analysis of SNPs from homologous fragments indicated that Pseudotsuga diverged from Pinus and Picea 167.26–149.19 million years ago. Analysis using the isolation-with-migration model identified significant signals of two-way gene flow between Pinus taeda and Pinus elliottii (P<0.001), while the isolation-with-initial-migration model suggested that introgression did not continue after this divergence. Gene flow has only ever occurred in the initial period of species divergence. Further analyses highlighted complex historical genome mixing and hybridization events over the evolution of the pine family. Thus, the divergence and radiation of the seven pines was a complex process accompanied by introgression and historical admixture.
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.
Abstract Background: Terpenoids are one of the most important compounds in plants, play an significant biological defense and developmental roles in numerous plant species, and widely used for industrial chemicals. Many previous studies have completed the identification of terpenoid biosynthetic pathway and related genes. However, few studies have focused on the molecular evolution analysis of terpenoid pathway genes in plants. In this study, we researched the evolutionary rate variation pattern of 16 terpenoid pathway genes in 12 species with a broad taxonomic span. Results: We retrieved 14 genes in MVA and MEP pathways and 2 extra genes from 12 species, respectively. The evolutionary parameters d N values and d N / d S ratios are varied significantly among genes, and the d N / d S ratios of most genes are varied substantially among lineages. The MVA and MEP pathways genes have different evolutionary rate variation pattern, although no significant difference in d N / d S ratios between two pathways genes. For MVA pathway, the downstream genes exhibits the greater d N / d S ratio than upstream genes. For MEP pathway, the three midstream genes evolves more rapidly than other genes, and most of MEP pathway genes were detected the signature of positive selection under random sites models. Moreover, the d N / d S ratios of MVA and MEP pathways genes are negatively correlated with pathway position and PPI, and coding sequence length, respectively. Conclusions: Taken together, the results indicated that the evolutionary rate variation of MVA pathway genes is mainly attributed to differential selective constraint rather than the positive selection. However, the differential selective constraint relaxation and positive selection collectively shaped the evolutionary rate heterogeneity of MEP pathway genes.
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