De novo transcriptome assembly of Schisandra chinensis Turcz. (Baill.)

Transcriptome-wide analysis of PIP reductase gene family identified a phenylpropene synthase crucial for the biosynthesis of dibenzocyclooctadiene lignans in Schisandra chinensis

Phenylpropenes, such as isoeugenol and eugenol, are produced as defend compounds, floral attractants, and flavor constituents by phenylpropene synthases belonging to the PIP reductase family. Moreover, isoeugenol is proposed to be involved in the biosynthesis of dibenzocyclooctadiene lignans, the main active compounds of Schisandra chinensis (Turcz.) Baill. fruits (SCF). S. chinensis, a woody vine plant, is widely used for its medicinal, horticultural, edible, and economic values. In this study, nine ScPIP genes were identified and characterized from the transcriptome datasets of SCF. The expression profiles revealed that ScPIP genes were differentially expressed during different developmental stages of SCF. Three ScPIPs were selected and cloned as candidate genes encoding phenylpropene synthases according to phylogenetic analysis. ScPIP1 was proved to function as isoeugenol synthase (IGS) and designated as ScIGS1 through in vivo functional characterization in Escherichia coli. Subcellular localization analysis demonstrated that ScIGS1 was localized in both the cytoplasm and nucleus. The three-dimensional (3D) model of ScIGS1 was obtained using homology modeling. Site-directed mutagenesis experiments revealed that the substitution of residues at positions 110 and 113 impacted the product specificity of ScIGS1 and the mutation of Lys157 to Ala abolishing catalytic function. Moreover, the kcat values of mutants were lower than that of ScIGS1 using a deep learning approach. In conclusion, this study provides a basis for further research on PIP reductases and the biosynthetic pathway of dibenzocyclooctadiene lignans.

Tissue-specific transcriptome and metabolome analyses reveal candidate genes for lignan biosynthesis in the medicinal plant Schisandra sphenanthera

Schisandra sphenanthera is an extremely important medicinal plant, and its main medicinal component is bioactive lignans. The S. sphenanthera fruit is preferred by the majority of consumers, and the root, stem, and leaf are not fully used. To better understand the lignan metabolic pathway, transcriptome and metabolome analyses were performed on the four major tissues of S. sphenanthera. A total of 167,972,229 transcripts and 91,215,760 unigenes with an average length of 752 bp were identified. Tissue-specific gene analysis revealed that the root had the highest abundance of unique unigenes (9703), and the leaves had the lowest (189). Transcription factor analysis showed that MYB-, bHLH- and ERF-transcription factors, which played important roles in the regulation of secondary metabolism, showed rich expression patterns and may be involved in the regulation of processes involved in lignan metabolism. In different tissues, lignans were preferentially enriched in fruit and roots by gene expression profiles related to lignan metabolism and relative lignan compound content. Furthermore, schisandrin B is an important compound in S. sphenanthera. According to weighted gene co-expression network analysis, PAL1, C4H-2, CAD1, CYB8, OMT27, OMT57, MYB18, bHLH3, and bHLH5 can be related to the accumulation of lignans in S. sphenanthera fruit, CCR5, SDH4, CYP8, CYP20, and ERF7 can be related to the accumulation of lignans in S. sphenanthera roots. In this study, transcriptome sequencing and targeted metabolic analysis of lignans will lay a foundation for the further study of their biosynthetic genes.

Model Species to Investigate the Origin of Flowers

The angiosperms, or flowering plants, arose at least 135 million years ago (Ma) and rapidly diversified to form over 300,000 species alive today. This group appears, however, to have separated from its closest living relatives, the extant gymnosperms, much earlier: over 300 Ma. Representatives of basally-diverging angiosperm lineages are of key importance to studies aimed at reconstructing the most recent common ancestor of living angiosperms, including its morphological, anatomical, eco-physiological and molecular aspects. Furthermore, evo-devo comparisons of angiosperms with living gymnosperms may help to determine how the many novel aspects of angiosperms, including those of the flower, first came about. This chapter reviews literature on the origin of angiosperms and focusses on basally-diverging angiosperms and gymnosperms that show advantages as potential experimental models, reviewing information and protocols for the use of these species in an evo-devo context. The final section suggests a means by which data from living and fossil groups could be integrated to better elucidate evolutionary events that took place on the long stem-lineage that apparently preceded the radiation of living angiosperms.

Integration of full-length transcriptomes and anthocyanin metabolite analysis for understanding fruit coloration mechanism in Schisandra chinensis

Coloration directly affects the commercial value of Schisandra chinensis fruits. The composition and content of anthocyanin determine the S. chinensis fruit coloration. However, the molecular mechanism of anthocyanin biosynthesis and regulation in this fruit remains unknown. In this study, we performed integrative full-length transcriptomics and targeted metabolomics analyses in S. chinensis fruits at four different developmental stages to elucidate the coloration mechanism. Cyanidin3-O-xyl-rutinoside is the key anthocyanin, which is responsible for the reddening of S. chinensis fruits, and its accumulation gradually accelerated from the 80th day after fluorescence. Overall, 122,289 unigenes with an average length of 2592 bp and an N50 of 4232 bp were obtained through single-molecule real-time sequencing; a total of 16,456 differentially expressed genes were identified. Moreover, 10 full-length structural genes related to anthocyanin biosynthesis were found to be significantly differentially expressed with fruit ripening. Moreover, 10 glycosyltransferases (GTs) that may possess the activities of anthocyanidin 3-O-glucosyltransferase, anthocyanidin 3-O-glucoside rhamnosyltransferase, and xylosyltransferases, which are involved in the final three steps for cyanidin3-O-xyl-rutinoside synthesis, were identified through phylogenetic analysis. Based on these findings, we constructed the complete anthocyanin biosynthetic pathway in S. chinensis fruits; five ScMYBs, three ScbHLHs, and two ScWD40s potentially involved in regulating anthocyanin biosynthesis in S. chinensis fruits were also selected. Our study provides the foundation for further research on the molecular mechanism of anthocyanin biosynthesis and regulation for improving the quality of S. chinensis fruits. The results of full-length transcriptomes would provide researchers with novel insights into the molecular cloning of enzymes and their activity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01179-3.

Isolation and Detection Methods of Plant miRNAs

Small RNAs (sRNAs) are RNAs of low abundance in organisms. Among sRNAs, miRNAs are included and represent approximately 10% of the total number of sRNAs. The isolation of sRNAs is critical for miRNA detection and analysis. The precipitation of low-molecular-weight (LMW) RNAs from total RNA extracts has allowed enrichment of sRNAs. Here, we describe a simple method to isolate sRNAs from different plant species. The main advantage of this method is that it does not need first an extraction of total RNA and it is not based on TRIzol^® reagent. This method has been successfully used for miRNA analyses by Northern blot assay and RT-qPCR (these techniques are as well described in this chapter), as well as sRNA library preparation.