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

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)...

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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
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cited_by cdi_FETCH-LOGICAL-c692t-cf5a4099c682965a82446ebe4e2e4cbd5a652240dfa3a2c8bac61904db6835723
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container_title PloS one
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creator 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
description 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/.
doi_str_mv 10.1371/journal.pone.0061127
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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. 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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/.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23658685</pmid><doi>10.1371/journal.pone.0061127</doi><tpages>e61127</tpages><oa>free_for_read</oa></addata></record>
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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
title Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum
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