Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all of the sequenced basidiomycetes. In all, 24 physical CYP gene clusters are identified. Moreover, 78 CYP genes are coexpressed with lanosterol synthase, and 16 of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the G. lucidum genome makes this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi.

BackgroundInternal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns.Methodology/Principal FindingsIn this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level.ConclusionsIdentification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.

Panax ginseng C.A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6%) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.

The present study aimed to explore the holistic mechanism for the antihypertrophic effect of a compound in Chinese medicine, QiShenYiQi Pills (QSYQ) and the contributions of its components to the effect in rats with cardiac hypertrophy (CH). After induction of CH by ascending aortic stenosis, rats were treated with QSYQ, each identified active ingredient (astragaloside IV, 3, 4-dihydroxy-phenyl lactic acid or notoginsenoside R1) from its 3 major herb components or dalbergia odorifera, either alone or combinations, for 1 month. QSYQ markedly attenuated CH, as evidenced by echocardiography, morphology and biochemistry. Proteomic analysis and western blot showed that the majority of differentially expressed proteins in the heart of QSYQ-treated rats were associated with energy metabolism or oxidative stress. Each ingredient alone or their combinations exhibited similar effects as QSYQ but to a lesser extent and differently with astragaloside IV and notoginsenoside R1 being more effective for enhancing energy metabolism, 3, 4-dihydroxy-phenyl lactic acid more effective for counteracting oxidative stress while dalbergia odorifera having little effect on the variables evaluated. In conclusion, QSYQ exerts a more potent antihypertrophic effect than any of its ingredients or their combinations, due to the interaction of its active components through a multi-component and multi-target mode.

Metabolomics has been used as a tool in disease diagnosis and phenotype prediction. A urinary metabolomic study based on GC-MS in combination with multivariate statistics was used here to classify between knee osteoarthritis (OA) and healthy controls. OPLS-DA of the spectral data showed distinct metabolic profile variations between OA patients and healthy controls and between two OA phenotypes. Differential metabolites reveal up-regulated TCA cycle associated with OA and histamine metabolism disorders accompanied with knee effusion symptoms. This metabolomic method is potentially applicable as a novel strategy for OA diagnosis and patient stratification.