| Based on the information provided by structural genomics and the application of high throughput, large-scale analysis, functional genomics is a comprehensive way of study in gene expression, regulation and function, as well as to explore relationship and laws between genes, genes and proteins, and both with the growth and development at the level of genome. Biological research is increased from a single gene or protein to the genome based on functional genomics, while a lot of genes and proteins are systematically studied at the same time. Clarification the pathways and regulation of secondary metabolic pathway is one of the main contents of functional genomics in medicinal plants. Ginseng, American ginseng and yew are three medicinal plants with significantly medical and economic value and the main active ingredients are terpenoids. The three medicinal plants were selected for the study in this paper, from micro and macro perspectives, using functional genomics methods and geographic information system technology, respectively. Studies have focused on the transcriptome analysis, medicinal natural product biosynthesis, the key enzyme gene cloning and identification, and producing area suitability, respectively.American ginseng (Panax quinquefolius L.) for the Araliaceae (Araliaceae) are one of valuable medicinal herbs in the world and its roots are used as medicine, with the promotion of memory, anti-cancer, lowering blood pressure, blood fat, anti-fatigue, anti-diabetic, cardiac, sedative and other pharmacological effects. However, because of slow growth and succession cropping obstacles, the development of American ginseng as medicinal resources is extremely limited. The major bioactive phytochemicals responsible for this plant's pharmacological features are ginsenosides. Thus far, little is known regarding the genes involved in ginsenosides biosynthesis in this species. In this study, we generated 6678 expressed sequence tags (ESTs) from the flower, leaf, and root cDNA libraries of American ginseng. Assembly of ESTs resulted in 3349 unigenes including 534 contigs (with ESTs number ranging from 2 to 52) and 2815 singletons. By analyzing the predominant transcripts within specific tissues, a gene expression pattern was obtained in a tissue-specific manner. They were assigned according to the functional classification of unigenes to broad ranges of Gene Ontology (GO) categories which include biological processes, cellular components and molecular functions. Based on BLASTX search results,24 unigenes representing candidates related to ginsenosides biosynthesis were identified. Cloning and characterization of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR, EC:1.1.1.34), the rate-limiting enzyme in mevalonic acid (MVA) pathway, demonstrated that it belonged to the plant HMGR family and was highly expressed in leaves. Putative transcription factors were detected in 63 unigenes, including zinc finger, WRKY, homeobox and MADS-box family proteins. Five hundred eighty eight SSR motifs were identified, of which, dimer was the most abundant motif. These data will provide useful information on transcript profiles, gene discovery, transcriptional regulation, flower biogenesis, and marker-assisted selections. The analysis and information from this study will greatly contribute to the improvement of this medicinal plant as well as of other species in the Araliaceae family, for the purpose of ensuring adequate drug resources.Taxus species are highly valued both as renewable resources for the production of Taxol and as important trees for biodiversity conservation within the Northern Hemisphere. Thus far, few genomic or transcriptomic data are available for the members of this genus as demonstrated by only 179 expressed sequence tags (ESTs) in GenBank. In this study,81,148 high-quality reads from the needles of Taxus cuspidata were produced using the Roche GS FLX Titanium system. A total of 20,557 unique sequences were obtained, including 12,975 singletons and 7,582 contigs, with EST numbers ranging from 2 to 2,051. A total of 14,095 (68.6%) unique sequences shared a significant similarity to the sequences in public databases and have orthologs in other organisms. Gene Ontology revealed 11,220 (54.6%) unique sequences that could be assigned to 45 vocabularies. In the Kyoto Encyclopedia of Genes and Genomes mapping,2,403 transcripts were established as associated with 3,821 biochemical pathways. All enzymes in the plastidial 2-C-methyl-D-erythritol 4-phosphate pathway were well represented together with 8 of the 12 characterized enzymes involved in Taxol biosynthesis. Data mining homologues correlated with the putative remaining steps revealed candidates of cytochrome P450, epoxidase, coenzyme A ligase, and N-benzoyltransferase in the data sets. In total,291 transcripts were identified, representing putative homologues of a wide array of transcription factor families. There was also 753 simple sequence repeat motifs identified, of which hexamer was the most abundant motif. In the meantime, the results of this study revealed that a substantial number of transcripts had no obvious orthologs to known databases and might represent peculiar transcripts within the Taxus. These results provide the largest EST collections in Taxus and are essential for future efforts of gene discovery, functional genomics, and genome annotation in related species.In order to provide scinetific evidences for screening potential areas suitable for growing Chinses Shizhu Panax, adaptability and associated growing areas of its were analyzed using TCMGIS. Based on the optimum ecological data collected from Kuandian County, Liaoning Province, a geographic information system was established to analyze the adaptability of potential areas suitable for growing Chinses Shizhu Panax. Results showed that fifteen of areas under investigation enjoyed a similarity index of 95-100%, which adds up to 15943.93 km2 in area. These most adaptive areas mainly located in Liaoning Province and Jilin Province, which accounted for 96.44% and 3.56%, respectively. Results also showed that twenty two of areas under investigation having a similarity index of 90-95%, which adds up to 20070.83 km2 in area. These adaptive areas mainly located in Liaoning Province, Henan Province, Shanxi Province, and Jilin Province, which accounted for 73.88%,16.02%,9.78%, and 3.2%, respectively. The results went along with the current growing areas. Meanwhile, the potential growing regions had been identified by TCMGIS. The results in current study demonstrated the rationality and reliability of TCMGIS. The finding provides important evidances for the P. ginseng cultivation planning, protecting fine varieties, and growing the species under national standards.Data derived from present study will provide theoretical support for the research of functional genomics in medicinal plants and will lead to better utilization and development of natural medicinal resources in the future for the purpose of drug improvement. |
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