MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea

Yan-Liang Lin; Li-Ting Ma; Yi-Ru Lee; Shih-Shun Lin; Sheng-Yang Wang; Tun-Tschu Chang; Jei-Fu Shaw; Wen-Hsiung Li; Fang-Hua Chu

doi:10.1371/journal.pone.0123245

MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea

PLoS One. 2015 Apr 10;10(4):e0123245. doi: 10.1371/journal.pone.0123245. eCollection 2015.

Authors

Yan-Liang Lin¹, Li-Ting Ma¹, Yi-Ru Lee¹, Shih-Shun Lin², Sheng-Yang Wang³, Tun-Tschu Chang⁴, Jei-Fu Shaw⁵, Wen-Hsiung Li⁶, Fang-Hua Chu⁷

Affiliations

¹ School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan.
² Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
³ 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.
⁴ Division on Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan.
⁵ Department of Biological Science & Technology, I-Shou University, Kaohsiung, Taiwan.
⁶ Biodiversity Research Center, Academia Sinica, Taipei, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.
⁷ School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan; Experimental Forest, National Taiwan University, Nan-Tou, Taiwan.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Antrodia / genetics*
Antrodia / growth & development*
Antrodia / metabolism
Base Sequence
Gene Expression Profiling
Gene Expression Regulation, Developmental
Gene Expression Regulation, Fungal
Gene Ontology
Genome, Fungal
High-Throughput Nucleotide Sequencing
MicroRNAs / chemistry
MicroRNAs / genetics*
Molecular Sequence Data
Nucleic Acid Conformation
RNA, Fungal / chemistry
RNA, Fungal / genetics*

Substances

MicroRNAs
RNA, Fungal

Grants and funding

This work was supported by the National Science Council (NSC-101-2911- I-005-301, NSC-102-2911- I-005-301), and the Ministry of Education, Taiwan, under the Development Plan for World Class University and Research Centers of Excellence plan.