title: Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible FungusPleurotus ostreatus.
abstract: Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) ofPleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs inP. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved inP. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs ofP. ostreatuswere not conserved across Agaricomycotina fungi.
authors.affiliation: Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
authors.forename: Jibin
authors.identifier: 0000-0002-2544-6223
authors.initials: J
authors.lastname: Qu
authors.affiliation: Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
authors.forename: Mengran
authors.initials: M
authors.lastname: Zhao
authors.affiliation: School of Environmental Sciences, University of Guelph, Guelph, ON, Canada.
authors.forename: Tom
authors.initials: T
authors.lastname: Hsiang
authors.affiliation: College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Micro & Nano Research Institute of IC and System Applications, Shenzhen, Guangdong, China.
authors.forename: Xiaoxing
authors.initials: X
authors.lastname: Feng
authors.affiliation: Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
authors.forename: Jinxia
authors.identifier: 0000-0002-5232-8222
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China.
authors.forename: Chenyang
authors.identifier: 0000-0002-1956-6229
authors.initials: C
authors.lastname: Huang
mesh_terms: D016681:Genome, Fungal; D020076:Pleurotus / Q000235:genetics*; D012331:RNA, Fungal / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*
chemical_list: D012331:RNA, Fungal; D058727:RNA, Small Untranslated