title: MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea.
abstract: Antrodia cinnamomea, a precious, host-specific brown-rot fungus that has been used as a folk medicine in Taiwan for centuries is known to have diverse bioactive compounds with potent pharmaceutical activity. In this study, different fermentation states of A. cinnamomea (wild-type fruiting bodies and liquid cultured mycelium) were sequenced using the next-generation sequencing (NGS) technique. A 45.58 Mb genome encoding 6,522 predicted genes was obtained. High quality reads were assembled into a total of 13,109 unigenes. Using a previously constructed pipeline to search for microRNAs (miRNAs), we then identified 4 predicted conserved miRNA and 63 novel predicted miRNA-like small RNA (milRNA) candidates. Target prediction revealed several interesting proteins involved in tri-terpenoid synthesis, mating type recognition, chemical or physical sensory protein and transporters predicted to be regulated by the miRNAs and milRNAs.
authors: School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan.
authors: Yan-Liang
authors: YL
authors: Lin
authors: School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan.
authors: Li-Ting
authors: LT
authors: Ma
authors: School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan.
authors: Yi-Ru
authors: YR
authors: Lee
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
authors: Shih-Shun
authors: SS
authors: Lin
authors: Department of Forestry, National Chung-Hsing University, Taichun, Taiwan; Agricultural, Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Agricultural Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan.
authors: Sheng-Yang
authors: SY
authors: Wang
authors: Division on Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan.
authors: Tun-Tschu
authors: TT
authors: Chang
authors: Department of Biological Science & Technology, I-Shou University, Kaohsiung, Taiwan.
authors: Jei-Fu
authors: JF
authors: Shaw
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
authors: Wen-Hsiung
authors: WH
authors: Li
authors: School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan; Experimental Forest, National Taiwan University, Nan-Tou, Taiwan.
authors: Fang-Hua
authors: FH
authors: Chu
mesh_terms: D055491:Antrodia / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D001483:Base Sequence; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D015966:Gene Expression Regulation, Fungal; D063990:Gene Ontology; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012331:RNA, Fungal