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International Journal of Medicinal Mushrooms
IF: 1.423 5-Year IF: 1.525 SJR: 0.433 SNIP: 0.661 CiteScore™: 1.38

ISSN Print: 1521-9437
ISSN Online: 1940-4344

International Journal of Medicinal Mushrooms

DOI: 10.1615/IntJMedMushrooms.v17.i8.80
pages 783-797

Bioinformatic Identification of Potential MicroRNAs and Their Targets in the Lingzhi or Reishi Medicinal Mushroom Ganoderma lucidum (Higher Basidiomycetes)

Dashuai Mu
College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, People's Republic of China; College of Marine Science, Shandong University (Weihai), Weihai, People's Republic of China
Chenyang Li
College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, People's Republic of China
Liang Shi
Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Jiangsu, Nanjing, People's Republic of China
Xuchen Zhang
College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, People's Republic of China
Ang Ren
Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, People's Republic of China
Ming-Wen Zhao
Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Jiangsu, Nanjing, People's Republic of China

ABSTRACT

MicroRNAs (miRNAs) are a class of small, endogenous, noncoding RNA molecules that negatively regulate gene expression at the transcriptional or the post-transcriptional level. Although a large number of miRNAs have been identified in many species, especially model plants and animals, miRNAs in fungi remain largely unknown. In this study, based on a database of expressed sequence tags in Ganoderma lucidum, 89 potential miRNAs were identified using computational methods. Real-time polymerase chain reaction analysis of miRNA-like samples prepared from G. lucidum at different development stages revealed that miRNA-like RNAs were differentially expressed in different stages. Furthermore, a total of 28 potential targets were found based on near-perfect or perfect complementarity between the randomly selected 9 miRNA-like RNAs and the target sequences, and potential targets for G. lucidum miRNA-like RNAs were predicted. Finally, we studied the expression pattern of 4 target genes in 3 different development stages of G. lucidum to further understand the mechanism of interaction between miRNA-like RNAs and their target genes. Our analysis paves the way toward identifying fungal miRNA-like RNAs that might be involved in various physiological and cellular differentiation processes.


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