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Background    Ganoderma lucidum  is a basidiomycete white rot fungus and is of medicinal importance in China, Japan and other countries in the Asiatic region. To date, much research has been performed in identifying the medicinal ingredients in  Ganoderma lucidum . Despite its important therapeutic effects in disease, little is known about  Ganoderma lucidum  at the genomic level. In order to gain a molecular understanding of this fungus, we utilized Illumina high-throughput technology to sequence and analyze the transcriptome of  Ganoderma lucidum .    Methodology/Principal Findings  We obtained 6,439,690 and 6,416,670 high-quality reads from the mycelium and fruiting body of  Ganoderma lucidum , and these were assembled to form 18,892 and 27,408 unigenes, respectively. A similarity search was performed against the NCBI non-redundant nucleotide database and a customized database composed of five fungal genomes. 11,098 and 8, 775 unigenes were matched to the NCBI non-redundant nucleotide database and our customized database, respectively. All unigenes were subjected to annotation by Gene Ontology, Eukaryotic Orthologous Group terms and Kyoto Encyclopedia of Genes and Genomes. Differentially expressed genes from the  Ganoderma lucidum  mycelium and fruiting body stage were analyzed, resulting in the identification of 13 unigenes which are involved in the terpenoid backbone biosynthesis pathway. Quantitative real-time PCR was used to confirm the expression levels of these unigenes.  Ganoderma lucidum  was also studied for wood degrading activity and a total of 22 putative FOLymes (fungal oxidative lignin enzymes) and 120 CAZymes (carbohydrate-active enzymes) were predicted from our  Ganoderma lucidum  transcriptome.    Conclusions  Our study provides comprehensive gene expression information on  Ganoderma lucidum  at the transcriptional level, which will form the foundation for functional genomics studies in this fungus. The use of Illumina sequencing technology has made de novo transcriptome assembly and gene expression analysis possible in species that lack full genome information.

Deep Insight into the Ganoderma lucidum by Comprehensive Analysis of Its Transcriptome