Bioinformatics Studies For Genetic Resource Of Medicinal Plants

Bioinformatics is an interdisciplinary involving biology, computer science, mathematics, and so on. Recently, molecular biology improved the development of bioinformatics, and they have been applied to the field of Traditional Chinense Medicine (TCM) and provide a new method for the study of TCM. In this study, bioinformatics was used to genomics, post-genomics and molecular identification for medicinal plants, some key bioinformatics methods were constructed.Genomics is the foundation to study medicinal plants systematically. In this study, key bioinformatics technologies were studied about genomics analysis. For genome assembly, overlap gragh method was used to build genome assembly pipeline, and we used optical mapping for validate and improve assembly. For example, we obtained48.9Mb Ganoderma sinense genome sequences, and twelve chromosomes. For gene prediction, HMM-based and evidence-based methods were used to gene prediction, the accuracy of gene prediction was improved. For gene functional annotation, a gene functional annotation pipeline was constructed using Smith-Waterman algorithm and HMM method. Genome structures between G. sinense and G. lucidum were compared using suffix tree method, the results showed their genome structures were mostly consistent, however, several structure variants were still found, which may be generated from chromsome rearrangement events. Estimating Ganoderma evolution time using the maximum likelihood method and fossil evidence, we found the divergence time of Ganoderma was estimated to be approximately38Ma (millions of years ago). In addition, we write a gene cluster mining algorithm, and1NRPS, five PKSs,13TPSs of gene clusters were identified in G. sinense genome using our gene cluster prediction pipeline.Post-genomics, also called functional genomics, mainly studies gene function and gene expression regulation. In this study, whole genome analysis were executed using bioinformatics technology for RNA editing, small RNAs and DNA methylation. Based on Negative binomial test, a differential expression analysis pipeline was built, differential expressed genes were classified based on GO and KEGG enrichment analysis. In G. sinense,76differential expressed genes were found involving the biogenesis of secondary metabolism. RNA editing regulates the gene expression by altering RNAs. In our results, based on single nucleotide variants, we write a RNA editing analysis pipeline, including the analysis of RNA editing type classification, RNA editing degree, annotation and enrichment analysis for edited genes. Another regulation mechanism was called as small RNA regulation, which silences gene expression by degrading transcription products. In this study, a pipeline of small RNA analysis was built, including small RNA classifiction, small RNA mapping, and targe gene prediction. In addtion, based on bisulfite sequencing, a DNA methylation analysis pipiline was written for recgnizing DNA methylation sites.Bioinformatics was used into DNA barcoding identification of medicinal plants, including identification algorithms and database, In this study, Sequence variants were estimated by caculating genetic distance in intra-and inter-species. DNA barcoding gap was used to validate the variants in intra-and inter-species. They can screen appropriate DNA barcode. BLAST method, based on Smith-Waterman algorithm, and Distance method, based on Needleman-Wunsch, were used to DNA barcoding identification. According to results, BLAST method can be used to fast and accurate DNA barcoding identification.Bioinformatics can be used to data storage, management and analysis by database construction. In this study, medicinal plant genome database and DNA barcoding system for identifying medicinal plants were built. For medicinal plant genome database, gene models and gene annotation were stored in MySQL database, genome browse can be used to show genome structure, gene location and transcriptome alignments. In this database, a gene cluster prediction tool was provided, a genome visualization tool can be used to view chromosome information. In addition, a DNA barcoding system for identifying medicinal plants were built using BLAST tool and computer programming language. This system include abundant herbal medicine and their adultrant from six pharmacopoeia, including Pharmacopoeia of the People’s Republic of China (PPRC), United States Pharmacopeia, Japanese Pharmacopoeia, Korean Pharmacopoeia, European Pharmacopoeia and Indian Pharmacopoeia. ITS2and psbA-trnH contain73,800sequences and31,241sequences, respectively.In this study, bioinformatics was applied into genomics, post-genomics and molecular identification for medicinal plants. For omics, bioinformatics methods were constructed, plenty of data and results can be used to post-genomics study. For molecular identification, BLAST method was used to DNA barcoding and database. In summary, bioinformatics can be widely used to traditional Chinense medicine study, its development in TCM will further improve the modernization and globalization of Traditional Chinese Medicine.