Transcriptomics Studies Of The Medicinal Plant Linicera Japonica Thumb And The Medicinal Fungus Paecilomyces Hepialid

Chinese medicine has a long history in our country. There is no clear validation of modern scientific theory, but thousands of years of clinical experience are the scientific experiments. However, with the development of next-generation sequencing methods and chemical analysis technology, people can study Chinese herbal medicinal ingredients, synthetic pathway and mechanism of action of compounds through modern experimental techniques. These studies results can make the Chinese medicine theries perfect. Through the transcriptome analysis, we can enrich the Chinese herbal medicine genetic information and find secondary metabolism and functional enzyme genes about important medicines.The herb Flos Lonicerae Japonicae (FLJ or Lonicera japonica Thunb.) is used as an anti-inflammatory agent but the chemical quality of FLJ and its medicinal efficacy has not been consistent. Here, we analyzed the transcriptomes and metabolic pathways to evaluate the active medicinal compounds in FLJ and hope that this approach can be used for a variety of medicinal herbs in the future. We assess transcriptomic differences between FLJ and L.japonica Thunb. var. chinensis (Watts)(rFLJ), which may explain the variable medicinal effects. We acquired transcriptomic data (over100million reads) from the two herbs, using RNA-seq method and the Illumina GAII platform. The transcriptomic profiles contain over6,000expressed sequence tags (ESTs) for each of the three flower development stages from FLJ, as well as comparable amount of ESTs from the rFLJ flower bud. To elucidate enzymatic divergence on biosynthetic pathways between the two varieties, we correlated genes and their expression profiles to known metabolic activities involving the relevant active compounds, including phenolic acids, flavonoids, terpenoids, and fatty acids. We also analyzed the diversification of genes that process the active compounds to distinguish orthologs and paralogs together with the pathways concerning biosynthesis of phenolic acid and its connections with other related pathways. Our study provides both an initial description of gene expression profiles in flowers of FLJ and its counterfeit rFLJ and the enzyme pool that can be used to evaluate FLJ quality. Detailed molecular-level analyses allow us to decipher the relationship between metabolic pathways involved in processing active medicinal compounds and gene expressions of their processing enzymes. Our evolutionary analysis revealed specific functional divergence of orthologs and paralogs, which lead to variation in gene functions that govern the profile of active compounds.Paecilomyces hepiali is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis anamorph stage. This fungus interacts with other fungi to synthesise chemically active constituents, such as purine nucleotides, polysaccharides and cordycepic acid. However, there is insufficient information on the metabolic mechanism of these active components. Therefore, high-throughput sequencing is needed to sequence a large amount of transcripts for gene discovery and functional analysis. Two samples, which varied in their culture time (four days vs. nine days) and showed differences in biomass and purine nucleotides synthesis, were used to evaluate the complete transcriptome. More than153million reads were generated using Illumina pair-end sequencing technology. After evaluating the quality of the raw sequencing reads, nearly132million reads were assembled into16,802Unigenes by Trinity. For annotation, all Unigenes were searched against the public database, and13,268(79.0%) were similar to known proteins. The species with the most shared sequence identity was Cordyceps militaries (10,272,75.4%of the total sequences). Out of these annotated sequences,9,475,9,897and3,215Unigenes were assigned to the Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COG) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) databases, respectively. In addition,1,375transcripts with enzyme commission numbers were assigned to288KEGG pathways. The coverage of transcripts was determined in terms of the fragments per kilobase of transcript per million mapped reads, and7,209Unigenes were differentially expressed between the two samples. After a chemical composition analysis, four putative critical enzyme genes for purine nucleotide metabolism were identified by quantitative real-time PCR. The transcriptional analysis of fungi during different fermentation phases provided a great deal of information about the genes and pathways involved in metabolism. This study generated a substantial number of Paecilomyces hepiali transcript sequences, which could be used to discover critical enzyme genes associated with purine nucleotide synthesis. In addition, these sequences are a valuable resource for the Cordyceps sinensis community.