Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum

• Published in: PloS one 2013-05, Vol.8 (5), p.e61127-e61127
• Main Authors: Huang, Yen-Hua, Wu, Hung-Yi, Wu, Keh-Ming, Liu, Tze-Tze, Liou, Ruey-Fen, Tsai, Shih-Feng, Shiao, Ming-Shi, Ho, Low-Tone, Tzean, Shean-Shong, Yang, Ueng-Cheng
• Format: Article
• Language: English
• Subjects: Alternative splicing; Alternative Splicing - genetics; Analysis; Antisense RNA; Bioactive compounds; Biological effects; Biology; Cell walls; Chemical synthesis; Cloning; Consortia; Data processing; DNA sequencing; Enzymes; Exons; Expressed sequence tags; Expressed Sequence Tags - metabolism; Fungi; Ganoderma lucidum; Gene expression; Gene Library; Genes; Genes, Fungal - genetics; Genetic aspects; Genomes; Genomics; Introns; Medical research; Mushrooms; Mycelium - genetics; Nucleotide sequence; Plant pathology; Reishi - genetics; RNA, Messenger - genetics; RNA, Messenger - metabolism; Sequence Analysis; Synthetic biology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0061127

Ganoderma lucidum (G. lucidum) is a medicinal mushroom renowned in East Asia for its potential biological effects. To enable a systematic exploration of the genes associated with the various phenotypes of the fungus, the genome consortium of G. lucidum has carried out an expressed sequence tag (EST) sequencing project. Using a Sanger sequencing based approach, 47,285 ESTs were obtained from in vitro cultures of G. lucidum mycelium of various durations. These ESTs were further clustered and merged into 7,774 non-redundant expressed loci. The features of these expressed contigs were explored in terms of over-representation, alternative splicing, and natural antisense transcripts. Our results provide an invaluable information resource for exploring the G. lucidum transcriptome and its regulation. Many cases of the genes over-represented in fast-growing dikaryotic mycelium are closely related to growth, such as cell wall and bioactive compound synthesis. In addition, the EST-genome alignments containing putative cassette exons and retained introns were manually curated and then used to make inferences about the predominating splice-site recognition mechanism of G. lucidum. Moreover, a number of putative antisense transcripts have been pinpointed, from which we noticed that two cases are likely to reveal hitherto undiscovered biological pathways. To allow users to access the data and the initial analysis of the results of this project, a dedicated web site has been created at http://csb2.ym.edu.tw/est/.