Bioinformatics analysis and function prediction of ginseng TCP transcription factor family / 中国中药杂志

The longevity mechanism of ginseng(Panax ginseng) is related to its strong meristematic ability. In this paper, this study used bioinformatic methods to identify the members of the ginseng TCP gene family in the whole genome and analyzed their sequence characteristics. Then, quantitative real-time fluorescent PCR was performed to analyze the TCP genes containing elements rela-ted to meristem expression in the taproots, fibrous roots, stems, and leaves. According to the data, this study further explored the expression specificity of TCP genes in ginseng tissues, which facilitated the dissection of the longevity mechanism of ginseng. The ginseng TCP members were identified and analyzed using PlantTFDB, ExPASy, MEME, PLANTCARE, TBtools, MEGA and DNAMAN. The results demonstrated that there were 60 TCP gene family members in ginseng, and they could be divided into two classes: Class Ⅰ and Class Ⅱ, in which the Class Ⅱ possessed two subclasses: CYC-TCP and CIN-TCP. The deduced TCP proteins in ginseng had the length of 128-793 aa, the isoelectric point of 4.49-9.84 and the relative molecular mass of 14.2-89.3 kDa. They all contained the basic helix-loop-helix(bHLH) domain. There are a variety of stress response-related cis-acting elements in the promoter regions of ginseng TCP genes, and PgTCP20-PgTCP24 contained the elements associated with meristematic expression. The transcription levels of PgTCP20-PgTCP24 were high in fibrous roots and leaves, but low in stems, indicating the tissue-specific expression of ginseng TCP genes. The Class Ⅰ TCP members which contained PgTCP20-PgTCP23, may be important regulators for the growth and development of ginseng roots.

Cloning and expression analysis of GlPS1, GlPS2 gene in Glehnia littoralis / 中草药

Objective: To clone the full-length cDNA sequences of psoralen synthase (PS) genes from Glehnia littoralis so as to perform the bioinformatic and expression pattern analysis. Methods: Based on our previous transcriptome sequencing data of G. littoralis, the gene sequences GlPS1 and GlPS2 with high expression level were screened. The 3’cDNA ends of GlPS1 and GlPS2 genes were cloned by the RACE (rapid amplification of cDNA ends) method and the full-length cDNA of genes were assembled by using DNAMAN software. And then encoded GlPS proteins were analyzed by the bioinformatics tools. The issue specific expression of GlPS1 and GlPS2 genes were detected using qPCR. Results: The full-length cDNA of GlPS1 gene was 1 885 bp, which encoding a protein of 495 amino acids with a predicted molecular weight of 55 740.7 and isoelectric point of 8.28; The full-length cDNA of GlPS2 gene was 1 971 bp, which encoding a protein of 502 amino acids with a predicted molecular weight of 56 363.9 and isoelectric point of 6.62. GlPS1 and GlPS2 proteins belong to the cytochrome P450 superfamily, which share one transmembrane zone acting as hydrophilic protein. Phylogenetic analysis showed GlPS1 and GlPS2 were genetically closely related to the PS of Pastinaca sativa, Apium graveolens, Ammi majus. Higher expression of GlPS1 gene was observed in roots than leaves. However, GlPS2 gene was expressed at a relatively higher level in flowers than in roots. Conclusion: The full-length cDNA of GlPS1 and GlPS2 genes were obtained and the expression patterns were explored in G. littoralis for the first time, which provided a foundation for further studies on gene function and genetic regulatory mechanism of GlPS.

Cloning, subcellular localization and expression analysis of a transcription factor gene SmMYB87 in Salvia miltiorrhiza / 中草药

Objective To clone the R2R3 MYB transcription factor gene SmMYB87 in subgroup 14 from Salvia miltiorrhiza, and analyze the bioinformatics and expression of this gene. Methods Total RNA extracted from S. miltiorrhiza was used as cDNA synthesis template and the full length cDNA sequence was obtained through homology-based cloning and rapid amplification of cDNA ends (RACE) technology. The structure and physicochemical properties of SmMYB87 gene and its coded protein were analyzed with bioinformatics softwares. The expression of SmMYB87 in different organs was determined with qRT-PCR, and a GFP fusion expression vector was constructed to investigate the subcellular laicization of SmMYB87 protein. Results SmMYB87 gene contained two introns and an open reading frame (ORF) of 732 bp, encoding 243 amino acid polypeptides. It expressed in roots, stems, leaves and flowers with similar expression levels and the SmMYB87 protein located in nucleus and cytomembrane. Conclusion The analysis of sequence structure and expression pattern of SmMYB87 will be helpful to study the regulating roles of this gene in S. miltiorrhiza.