5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea Public Deposited

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Creator
  • Zolan, Miriam E
    • Other Affiliation: Department of Biology, Indiana University, Bloomington, Indiana, United States of America
  • Pukkila, Patricia J
    • Affiliation: College of Arts and Sciences, Department of Biology
  • Au, Chun Hang
    • Other Affiliation: Food Research Centre and Food and Nutrition Sciences Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, S.A.R., Hong Kong
  • Cheng, Chi Keung
    • Other Affiliation: Food Research Centre and Food and Nutrition Sciences Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, S.A.R., Hong Kong
  • Kwan, Hoi Shan
    • Other Affiliation: Food Research Centre and Food and Nutrition Sciences Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, S.A.R., Hong Kong
  • Stajich, Jason E
    • Other Affiliation: Department of Plant Pathology and Microbiology, University of California-Riverside, Riverside, United States of America
  • Wilke, Sarah K
    • Affiliation: College of Arts and Sciences, Department of Biology
Abstract
  • Abstract: Background: The transition from the vegetative mycelium to the primordium during fruiting body development is the most complex and critical developmental event in the life cycle of many basidiomycete fungi. Understanding the molecular mechanisms underlying this process has long been a goal of research on basidiomycetes. Large scale assessment of the expressed transcriptomes of these developmental stages will facilitate the generation of a more comprehensive picture of the mushroom fruiting process. In this study, we coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. Results: We evaluated the expression of >3,000 genes in the two respective growth stages and discovered that almost one-third of these genes were preferentially expressed in either stage. This identified a significant turnover of the transcriptome during the course of fruiting body development. Additionally, we annotated more than 79,000 transcription start sites (TSSs) based on the transcriptomes of the mycelium and stage 1 primoridum stages. Patterns of enrichment based on gene annotations from the GO and KEGG databases indicated that various structural and functional protein families were uniquely employed in either stage and that during primordial growth, cellular metabolism is highly up-regulated. Various signaling pathways such as the cAMP-PKA, MAPK and TOR pathways were also identified as up-regulated, consistent with the model that sensing of nutrient levels and the environment are important in this developmental transition. More than 100 up-regulated genes were also found to be unique to mushroom forming basidiomycetes, highlighting the novelty of fruiting body development in the fungal kingdom. Conclusions: We implicated a wealth of new candidate genes important to early stages of mushroom fruiting development, though their precise molecular functions and biological roles are not yet fully known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea.
Date of publication
Identifier
  • doi:10.1186/1471-2164-14-195
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Chi Keung Cheng et al.; licensee BioMed Central Ltd.
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Journal title
  • BMC Genomics
Journal volume
  • 14
Journal issue
  • 1
Page start
  • 195
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1471-2164
Bibliographic citation
  • BMC Genomics. 2013 Mar 20;14(1):195
Access
  • Open Access
Publisher
  • BioMed Central Ltd
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