Abstract
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 FindingsWe 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.ConclusionsOur 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.
Highlights
Ganoderma lucidum is a basidiomycete white rot fungi and has been used as traditional herbal medicine in Asia for thousands of years [1]
Illumina Sequencing and De novo Assembly To obtain an overview of the G. lucidum gene expression profiles during different developmental stages, cDNA samples were prepared from G. lucidum mycelia and fruiting bodies and sequenced using the Illumina HiSeqTM 2000 sequencing platform
GO categories ‘‘carbohydrate metabolism’’ (P#0.0001), ‘‘catabolism’’ (P#0.001), ‘‘electron transport’’ (P#0.05), ‘‘energy pathways’’ (P#0.01), ‘‘extracellular’’ (P#0.0001) and ‘‘carbohydrate binding’’ (P#0.0001) were overrepresented in fruiting body differentially expressed genes (DEGs). These results indicated that biosynthesis activity was much higher at the transcriptional level in mycelium compared with the fruiting body and that the carbohydrate metabolism is essential in G. lucidum fruiting bodies
Summary
Ganoderma lucidum is a basidiomycete white rot fungi and has been used as traditional herbal medicine in Asia for thousands of years [1] It has an abundance of bioactive components, which have numerous positive effects in diseases with little side effects [2,3,4,5]. Over 200 polysaccharides have been isolated from the fruiting bodies and mycelia of this fungus, among these, b-1–3 and b-1–6 D-glucans are the major bioactive components [10,13,14] Their multiple pharmacological effects, such as immunomodulation, antioxidation, antitumor activity and especially hepatoprotection against chemical or immune hepatic damage, have been demonstrated in numerous animal models [15,16,17,18]. 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
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