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.

Selection of Reference Genes for microRNA Real-time PCR Under Salt Stress in Armillaria gallica / 中国实验方剂学杂志

Objiective： In the process of microRNA expression analysis by quantitative Real-time polymerase chain reaction（Real-time PCR），the selection of miRNA plays an important role in data standardization. Method:In this paper，13 Armillaria gallica.Candidate miRNAs were selected for bioinformatics analysis of their precursors，and the PMRD was used to predict similar sequences of their precursors，and the RNAfold was used to predict the secondary structure of the candidate miRNAs and their similar sequences. Real-time PCR was used to detect miRNAs expression in two genotypes of Armillaria gallica（genotype A，genotype B） before and after salt stress，and geNorm，NormFinder and BestKeeper were used to analyze the stability of miRNAs expression. Result:Secondary structure prediction and characterization of 9 candidate miRNA precursors showed that the miRNA predicted belonged to the miR family with typical stem-loop structure and the mature miRNAs were at the 5' or 3' end of the miRNA precursors.geNorm analysis showed that genotype A Armillaria gallica could select Novel-4* and Novel-9 as reference gene，genotype B could select Novel-9 and Novel-16 as its reference gene.NormFinder analysis showed that Novel-9 was stable in both genotype A and B Armillaria gallica.BestKeeper analysis showed that Novel-12* was stable in genotype A Armillaria gallica and Novel-2* was stable in genotype B Armillaria gallica. Conclusion:miRNA Novel-9 is the best stable reference gene，which lays a foundation for further research on the regulation mechanism of miRNA in Armillaria gallica.