Metabolic and transcriptomic analyses reveal different metabolite biosynthesis profiles between leaf buds and mature leaves in Ziziphus jujuba mill

Combined Metabolome and Transcriptome Analyses Reveal the Flavonoids Changes and Biosynthesis Mechanisms in Different Organs of Hibiseu manihot L

Hibiseu manihot L. (Jinhuakui, JHK), also known as a garden landscape plant, is widely cultivated as a landscape plant having pharmacological effects due to its high flavonoids content. Although flavonoids were the main active pharmaceutical ingredients in JHK, little information was obtained about the content, composition, and accumulation pattern of flavonoids in different tissues. Most studies only identified a few kinds of flavonoids in JHK limited by separation and identification problems. Therefore, combined metabolome and transcriptome analysis was performed to explore the accumulation patterns and biosynthesis mechanisms of flavonoids in JHK. In this study, we identified 160 flavonoids in 15 samples of JHK (flower, leaf, root, stem, and seeds) by using LC-MS/MS. Consistent with the total flavonoid content determination, these flavonoids were significantly accumulated in flowers, followed by leaves, stems, roots, and seeds. Among them, certain flavonoids, with high content, were also identified for the first time in JHK, such as tricetin, catechin, hesperidin, ncyanidin-3-O-sambubioside, astragalin, procyanidin B2/B3/C1, apigenin-5-O-glucoside, etc. Different tissues underwent significantly reprogramming of their transcriptomes and metabolites changes in JHK, particularly in the flavonoid, flavone, and flavonol biosynthesis pathways. We conducted a correlation analysis between RNA-seq and LC-MS/MS to identify the key genes and related flavonoids compounds, rebuild the gene-metabolites regulatory subnetworks, and then identified 15 key genes highly related to flavonoids accumulation in JHK. These key genes might play a fine regulatory role in flavonoids biosynthesis by affecting the gene expression level in different organs of JHK. Our results could be helpful for the improvement of the market/industrial utilization value of different parts of JHK, to pave the way for the regulatory mechanism research of flavonoids biosynthesis, and provide insight for studying the production quality improvement of JHK.

Metabolomics and microbiome reveal potential root microbiota affecting the alkaloidal metabolome in Aconitum vilmorinianum Kom

Background

The plant microbiome is vital for plant health, fitness, and productivity. Interestingly, plant metabolites and the plant microbiome can influence each other. The combination of metabolomics and microbiome may reveal the critical links between the plant and its microbiome. It is of great significance to agricultural production and human health, especially for Chinese medicine research. Aconitum vilmorinianum Kom. is a herb with alkaloid activities, and its roots are the raw material for some Chinese medicines. Former studies have investigated alkaloidal metabolites and antibacterial activities of endophytes in A. vilmorinianum roots. However, there are limited reports on the root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum.

Results

This research used ultra performance liquid chromatography-tandem mass spectrometry technology and high-throughput sequencing to examine the alkaloidal metabolome, bacterial microbiota, and fungal microbiota in A. vilmorinianum roots at two different sites in China. The results revealed that the samples from the two sites were rich in distinct alkaloidal metabolites and recruited significantly different root microbiota. Based on bioinformatics analysis, we found the potential bacterial and fungal microbiota impacting the alkaloidal metabolome in A. vilmorinianum.

Conclusion

Our findings reveal the composition of the alkaloidal metabolome, bacterial root microbiota, and fungal root microbiota in A. vilmorinianum roots at two different sites. Potential root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum are indicated. This study provides a strategy for the cultivation and research of A. vilmorinianum and other Chinese herbs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02486-1.

Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change

Acer pseudosieboldianum (Pax) Komarov is an ornamental plant with prominent potential and is naturally distributed in Northeast China. Here, we obtained a chromosome-scale genome assembly of A. pseudosieboldianum combining HiFi and Hi-C data, and the final assembled genome size was 690.24 Mb and consisted of 287 contigs, with a contig N50 value of 5.7 Mb and a BUSCO complete gene percentage of 98.4%. Genome evolution analysis showed that an ancient duplication occurred in A. pseudosieboldianum. Phylogenetic analyses revealed that Aceraceae family could be incorporated into Sapindaceae, consistent with the present Angiosperm Phylogeny Group system. We further construct a gene-to-metabolite correlation network and identified key genes and metabolites that might be involved in anthocyanin biosynthesis pathways during leaf color change. Additionally, we identified crucial teosinte branched1, cycloidea, and proliferating cell factors (TCP) transcription factors that might be involved in leaf morphology regulation of A. pseudosieboldianum, Acer yangbiense and Acer truncatum. Overall, this reference genome is a valuable resource for evolutionary history studies of A. pseudosieboldianum and lays a fundamental foundation for its molecular breeding.

Integrated Metabolome and Transcriptome Analyses Reveal Dissimilarities in the Anthocyanin Synthesis Pathway Between Different Developmental Leaf Color Transitions in Hopea hainanensis (Dipterocarpaceae)

Changes in plant leaf color during development are directly related to the accumulation or degradation of certain phytochemicals such as anthocyanins. Since some anthocyanins can be beneficial to human health and provide insights into the biology of leaves, the underlying processes and timing by which plants produce these molecules has been the focus of numerous studies. The tree species Hopea hainanensis generally produces green leaves at all growth stages; however, a few explored individuals have been identified possessing red leaves on the top of the seedlings at a young stage. While the phenomenon of leaf color varying with age has been studied in several species, the underlying mechanisms are largely unknown in H. hainanensis. Using a metabolomics approach, the young red leaves in H. hainanensis were found to contain higher levels of anthocyanins and flavonoids than the young green-leaved individuals. Among anthocyanins, pelargonidin and cyanidin were the most likely candidates contributing to the red color of the young leaves. Transcriptome results indicated the genes related to the production of these anthocyanins were significantly upregulated, leading to greater accumulation of red pigments. Specifically, the expression of several MYB and bHLH genes in young red leaf lines was significantly higher than that in the young green leaf lines, especially HhMYB66, HhMYB91, HhMYB6, and HhbHLH70. As such these four transcription factors are probably the main regulatory genes resulting in young red leaves in H. hainanensis. From these results, comparative analyses with other species can be made to better understand the evolution of pigment biosynthesis and how anthocyanins function in plant metabolism and evolution/adaptation.

Profiling of Widely Targeted Metabolomics for the Identification of chemical composition in epidermis, xylem and pith of Gleditsiae spina

Gleditsiae spina, the thorn of Gleditsia sinensis Lam., has a long history of being used as a traditional medicine in East Asian countries. However, only a few biologically active substances have been identified from Gleditsiae spina. In this study, the epidermis, xylem and pith of Gleditsiae spina, respectively, namely Gs-E, Gs-X and Gs-P, were studied. We used a widely targeted metabolomics method to investigate the chemical composition in Gs-E, Gs-X and Gs-P. A total of 728 putative metabolites were identified from Gleditsiae spina, including 211 primary metabolites and 517 secondary metabolites. These primary and secondary metabolites could be categorized into more than 10 different classes. Flavonoids, phenolic acids, lipids, and amino acids and derivatives, and organic acids constituted the main metabolite groups. Multivariate statistical analysis showed that the Gs-E, Gs-X and Gs-P samples could be clearly separated. Differential accumulated metabolite (DAM) analysis revealed that more than half of the DAMs exhibited the highest relative concentrations in Gs-E, and most of the DAMs showed the lowest relative concentrations in Gs-X. Moreover, 11 common differential primary metabolites and 79 common differential secondary metabolites were detected in all comparison groups. These results further our understanding of chemical composition and metabolite accumulation of Gleditsiae spina.

Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Leaf Color Change in Chokecherry (Padus virginiana)

Chokecherry (Padus virginiana L.) is an important landscaping tree with high ornamental value because of its colorful purplish-red leaves (PRL). The quantifications of anthocyanins and the mechanisms of leaf color change in this species remain unknown. The potential biosynthetic and regulatory mechanisms and the accumulation patterns of anthocyanins in P. virginiana that determine three leaf colors were investigated by combined analysis of the transcriptome and the metabolome. The difference of chlorophyll, carotenoid and anthocyanin content correlated with the formation of P. virginiana leaf color. Using enrichment and correlation network analysis, we found that anthocyanin accumulation differed in different colored leaves and that the accumulation of malvidin 3-O-glucoside (violet) and pelargonidin 3-O-glucoside (orange-red) significantly correlated with the leaf color change from green to purple-red. The flavonoid biosynthesis genes (PAL, CHS and CHI) and their transcriptional regulators (MYB, HD-Zip and bHLH) exhibited specific increased expression during the purple-red periods. Two genes encoding enzymes in the anthocyanin biosynthetic pathway, UDP glucose-flavonoid 3-O-glucosyl-transferase (UFGT) and anthocyanidin 3-O-glucosyltransferase (BZ1), seem to be critical for suppressing the formation of the aforesaid anthocyanins. In PRL, the expression of the genes encoding for UGFT and BZ1 enzymes was substantially higher than in leaves of other colors and may be related with the purple-red color change. These results may facilitate genetic modification or selection for further improvement in ornamental qualities of P. virginiana.

Exploring the genic resources underlying metabolites through mGWAS and mQTL in wheat: From large-scale gene identification and pathway elucidation to crop improvement

Common wheat (Triticum aestivum L.) is a leading cereal crop, but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize. The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets. Meanwhile, the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals. One such productive avenue is combining metabolomics approaches with genetic designs. However, this trial is not as widespread as that for sequencing technologies, especially when the acquisition, understanding, and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized. In this review, we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes. Considerable progress has been made in delivering improved varieties, suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and, as such, this procedure could serve as an -omics-informed roadmap for executing similar improvement strategies in wheat and other species.