Applied Microbiology and Biotechnology

, Volume 97, Issue 11, pp 4977–4989 | Cite as

Transcriptome analysis of candidate genes and signaling pathways associated with light-induced brown film formation in Lentinula edodes

  • Li-hua Tang
  • Hua-hua Jian
  • Chun-yan Song
  • Da-peng Bao
  • Xiao-dong Shang
  • Da-qiang Wu
  • Qi TanEmail author
  • Xue-hong ZhangEmail author
Genomics, transcriptomics, proteomics


High-throughput Illumina RNA-seq was used for deep sequencing analysis of the transcriptome of poly(A)+ RNA from mycelium grown under three different conditions: 30 days darkness (sample 118), 80 days darkness (313W), and 30 days darkness followed by 50 days in the light (313C), in order to gain insight into the molecular mechanisms underlying the process of light-induced brown film (BF) formation in the edible mushroom, Lentinula edodes. Of the three growth conditions, BF formation occurred in 313C samples only. Approximately 159.23 million reads were obtained, trimmed, and de novo assembled into 31,511 contigs with an average length of 1,746 bp and an N 50 of 2,480 bp. Based on sequence orientations determined by a BLASTX search against the NR, Swiss-Prot, COG, and KEGG databases, 24,246 (76.9 %) contigs were assigned putative descriptions. Comparison of 313C/118 and 313C/313W expression profiles revealed 3,958 and 5,651 significantly differentially expressed contigs (DECs), respectively. Annotation using the COG database revealed that candidate genes for light-induced BF formation encoded proteins linked to light reception (e.g., WC-1, WC-2, phytochrome), light signal transduction pathways (e.g., two-component phosphorelay system, mitogen-activated protein kinase pathway), and pigment formation (e.g., polyketide synthase, O-methyltransferase, laccase, P450 monooxygenase, oxidoreductase). Several DECs were validated using quantitative real-time polymerase chain reaction. Our report is the first to identify genes associated with light-induced BF formation in L. edodes and represents a valuable resource for future genomic studies on this commercially important mushroom.


Lentinula edodes Light-induced brown film formation Transcriptome Differential expression 



We thank Dr. Yin-bing Bian, Huazhong Agriculture University, for the culture experiments and technical support and Dr. John Buswell, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, for the linguistic revision of the manuscript. This research was supported by the National Natural Science Foundation of China (grant no. 31170098), the Science and Technology Commission of the Shanghai Municipality (grant no. 10391900900), the China National Key Basic Research Program (no. 2012CB721005), and Special Capital (Edible Fungi) for the Construction of a Modern Agriculture Industry Technical System, Ministry of Agriculture of China.

Supplementary material

253_2013_4832_MOESM1_ESM.pdf (281 kb)
ESM 1 (PDF 281 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Li-hua Tang
    • 1
    • 2
  • Hua-hua Jian
    • 1
  • Chun-yan Song
    • 2
  • Da-peng Bao
    • 2
  • Xiao-dong Shang
    • 2
  • Da-qiang Wu
    • 1
  • Qi Tan
    • 2
    Email author
  • Xue-hong Zhang
    • 1
    Email author
  1. 1.State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople’s Republic of China
  2. 2.National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiPeople’s Republic of China

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