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.
Highlights
MicroRNAs are a group of small non-coding RNAs commonly 21–22 nucleotides in length that have important roles in the post-transcriptional regulation of gene expression in plants and animals
Imprecise pairing of miRNA and the specific target genes leads to translational inhibition, and in plants the near perfect complementarity between miRNAs and their targets leads to messenger RNA cleavage [3,4]
RNA interference (RNAi)-related gene silencing in fungi was first described in Neurospora crassa in 1992 [5]
Summary
MicroRNAs (miRNAs) are a group of small non-coding RNAs commonly 21–22 nucleotides (nt) in length that have important roles in the post-transcriptional regulation of gene expression in plants and animals. They regulate a wide range of cellular processes including multicellular development, differentiation, apoptosis and stress response [1,2]. Mature miRNA regulates target gene expression negatively through complementary binding to coding sequences or the untranslated regions. RNA interference (RNAi)-related gene silencing in fungi was first described in Neurospora crassa in 1992 [5]. RNAi pathways use three major types of small noncoding RNAs, small interference RNAs (siRNAs), microRNAs (miRNAs) and PLOS ONE | DOI:10.1371/journal.pone.0123245. RNAi pathways use three major types of small noncoding RNAs, small interference RNAs (siRNAs), microRNAs (miRNAs) and PLOS ONE | DOI:10.1371/journal.pone.0123245 April 10, 2015
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