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Open Access Highly Accessed Research article

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

Chi Keung Cheng1, Chun Hang Au1, Sarah K Wilke2, Jason E Stajich3, Miriam E Zolan4, Patricia J Pukkila2 and Hoi Shan Kwan1*

Author Affiliations

1 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

2 Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

3 Department of Plant Pathology and Microbiology, University of California-Riverside, Riverside, United States of America

4 Department of Biology, Indiana University, Bloomington, Indiana, United States of America

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BMC Genomics 2013, 14:195  doi:10.1186/1471-2164-14-195

Published: 20 March 2013

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.

Keywords:
Coprinopsis cinerea; SAGE; Transcriptome; Microarray; Transcription start site; Fruiting body; Mycelium; Primordium