title: Bioinformatic Identification of Potential MicroRNAs and Their Targets in the Lingzhi or Reishi Medicinal Mushroom Ganoderma lucidum (Higher Basidiomycetes).
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.
authors.affiliation: 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;College of Marine Science.
authors.forename: Da-Shuai
authors.initials: DS
authors.lastname: Mu
authors.affiliation: 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.
authors.forename: Chenyang
authors.initials: C
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Liang
authors.initials: L
authors.lastname: Shi
authors.affiliation: 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.
authors.forename: Xuchen
authors.initials: X
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Ang
authors.initials: A
authors.lastname: Ren
authors.affiliation: 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.
authors.forename: Ming-Wen
authors.initials: MW
authors.lastname: Zhao
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D055029:Inverted Repeat Sequences; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012331:RNA, Fungal / Q000378:metabolism*; D020940:Reishi / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012331:RNA, Fungal