Project description:<p>Ganoderma is a class of medicinal fungi with diverse medicinal effects, of which triterpenoids are one of the main pharmacologically active substances. In this study, sporocarps of two Ganoderma species (G. leucocontextum, a newly discovered species, and G. lucidum, a traditional medicinal species) at five different developmental stages were used as test materials for joint transcriptomic and metabolomic analyses. Metabolomic analysis via Ultra-High Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS/MS) identified a total of 514 differential metabolites (screened by VIP 1 and P < 0.05). Among these, triterpenoids were the primary class of differentially abundant metabolites between the two species: G. leucocontextum consistently contained higher levels of ganoleucoin during development, while G. lucidum maintained higher levels of ganoderic acid. Transcriptomic analysis yielded 227.61 Gb of clean data (Q30 base percentage > 93%), with 228,593 significantly differentially expressed genes (DEGs) identified across the five developmental stages. Most genes in the triterpenoid synthesis pathway (including several Ganoderma-specific CYP450 family genes) were more highly expressed in G. lucidum. RT-qPCR validation of 6 key DEGs confirmed that their expression trends were consistent with transcriptomic data. Additionally, 6 putative transcription factors (belonging to HSF and GNAT families) potentially involved in Ganoderma triterpene metabolism were identified. Our findings provide datasets on dynamic gene expression and differential metabolites during the development of the two Ganoderma species, laying a foundation for subsequent in-depth research.</p>
Project description:Ganoderma colossum (Fr.) Baker, a white rot fungus distributed in tropical and subtropical forests, is a rare Ganoderma mushroom belonging to the family Ganodermataceae. In Asia, the fruiting body of G. colossum has been used as tonics or as folk medicine for a variety of illnesses, including malignant diseases. Colossolactone H (colo H) as a new compound was isolated and studied for its anticancer mechanism in human lung cancer H1650 cells. We used microarrays to analyze the gene expression changes upon colo H treatment that helped underlying the molecular mechanism of colo H in H1650 lung cancer cells. The H1650 cells treated with colo H for 12 and 24 h for RNA extraction and hybridization on Affymetrix microarrays.
Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.