Selection of Reference Genes for Expression Analysis in Chinese Medicinal Herb Huperzia serrata

Profiles of Metabolic Genes in Uncaria rhynchophylla and Characterization of the Critical Enzyme Involved in the Biosynthesis of Bioactive Compounds-(iso)Rhynchophylline

Rhynchophylline (RIN) and isorhynchophylline (IRN), two of the representative types of indole alkaloids, showed the unique spiroindole structures produced in Uncaria rhynchophylla. As the bioactive constituent of U. rhynchophylla, IRN has recently drawn extensive attention toward antihypertensive and neuroprotective activities. Despite their medicinal importance and unique chemical structure, the biosynthetic pathways of plant spiroindole alkaloids are still largely unknown. In this study, we used U. rhynchophylla, extensively used in traditional Chinese medicine (TCM), a widely cultivated plant of the Uncaria genus, to investigate the biosynthetic genes and characterize the functional enzymes in the spiroindole alkaloids. We aim to use the transcriptome platform to analyse the tissue-specific gene expression in spiroindole alkaloids-producing tissues, including root, bud, stem bark and leaf. The critical genes involved in the biosynthesis of precursors and scaffold formation of spiroindole alkaloids were discovered and characterized. The datasets from this work provide an essential resource for further investigating metabolic pathways in U. rhynchophylla and facilitate novel functional enzyme characterization and a good biopharming approach to spiroindole alkaloids.

Identification and Validation of Reference Genes for Gene Expression Analysis in Different Development Stages of Amylostereum areolatum

A strict relationship exists between the Sirex noctilio and the Amylostereum areolatum, which is carried and spread by its partner. The growth and development of this symbiotic fungus is key to complete the life history of the Sirex woodwasp. Real-time quantitative polymerase chain reaction (RT-qPCR) is used to measure gene expression in samples of A. areolatum at different growth stages and explore the key genes and pathways involved in the growth and development of this symbiotic fungus. To obtain accurate RT-qPCR data, target genes need to be normalized by reference genes that are stably expressed under specific experimental conditions. In our study, the stability of 10 candidate reference genes in symbiotic fungal samples at different growth and development stages was evaluated using geNorm, NormFinder, BestKeeper, delta Ct methods, and RefFinder. Meanwhile, laccase1 was used to validate the stability of the selected reference gene. Under the experimental conditions of this study, p450, CYP, and γ-TUB were identified as suitable reference genes. This work is the first to systematically evaluate the reference genes for RT-qPCR results normalization during the growth of this symbiotic fungus, which lays a foundation for further gene expression experiments and understanding the symbiotic relationship and mechanism between S. noctilio and A. areolatum.

Reference gene selection for real-time quantitative PCR assays in different tissues of Huperzia serrata based on full-length transcriptome sequencing

Huperzia serrata (H. serrata) produces various types of effective lycopodium alkaloids, especially Huperzine A (HupA), which is a promising drug for the treatment of Alzheimer's disease. Numerous studies focused on the chemistry, bioactivities, toxicology, and clinical trials of HupA; however, the public genomic and transcriptomic resources are very limited for H. serrata research, especially for the selection of optimum reference genes. Based on the full-length transcriptome datasets and previous studies, 10 traditional and three new candidate reference genes were selected in different tissue of H. serrata. Then, two optimal reference genes GAPDHB and HisH2A were confirmed by four analysis methods. In order to further verify the accuracy of the two reference genes, they were used to analyze the expression patterns of four HupA-biosynthetic genes (lysine decarboxylas, RS-norcoclaurine 6-O-methyltransferase, cytochrome P45072A1, and copper amine oxidase). The data suggested that the expression pattern of HupA-biosynthetic genes was consistent with them in transcriptome sequencing in different tissue of H. serrata. This study identified that GAPDHB and HisH2A provides the reliable normalization for analyzing the HupA biosynthetic gene expression in different tissues of H. serrata on the transcriptional level.

Evaluation of candidate reference genes for quantitative RTqPCR analysis in goldfish (Carassius auratus L.) in healthy and CyHV-2 infected fish

The accuracy of quantitative real time PCR (RTqPCR) can be attained only when a suitable reference gene is used. The gene expression for a particular gene may vary within different cells at different conditions. Hence, the suitability and stability of various potential reference genes have to be determined for expression studies. In this study, we have examined the potential of four different reference genes including β-Actin (ACTB), 18S ribosomal RNA (18S), glyceraldehyde-3P-dehydrogenase (GAPDH), and elongation factor 1 alpha (EF1A_A) in seven different tissues including gill, liver, kidney, spleen, heart, muscle and intestine of goldfish (Carassius auratus). The housekeeping genes were analyzed from healthy fish and in CyHV-2 challenged fish. Based upon the real time PCR results the gene expression varied among the genes and in tissues. The expression levels of the housekeeping genes were then compared and evaluated with the RefFinder web tool which analyses results using four different algorithms - BestKeeper, delta Ct, geNorm and NormFinder. EF1A_A was ranked to be the best gene in healthy fish by BestKeeper and geNorm analysis. The delta Ct and NormFinder algorithm have found 18S to be a stable gene in healthy fish but 18S was given to be least expressed in challenged fish. ACTB was also given as a stable gene by geNorm analysis in both healthy and challenged fish. Also, in CyHV-2 challenged fish, EF1A_A was identified as the best gene by all the three analysis except by BestKeeper analysis, where it has ranked GADPH as the best housekeeping gene. Expression of the four candidate reference genes differed across all tissue types tested, inferring that a thorough study of the reference genes is necessary for cross tissue comparison. These results can be further used in the immune gene response study of goldfish infected with any viral pathogen to develop better health strategies in the disease management of goldfish aquaculture.