Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus 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) of Pleurotus 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 in P. 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 in P. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs of P. ostreatus were not conserved across Agaricomycotina fungi.

Figure 1

The ideogram showing the genomic features of P. ostreatus. (a) Scaffolds longer than 10 kbp. (b) GC content: the percentage of G+C in 10 kbp nonoverlapping windows. (c) Gene density: the number of genes in 10 kbp nonoverlapping windows. (d) Distribution of tRNAs. (e) Distribution of miRNAs. (f) Distribution of snRNAs, snoRNAs, and others.

Figure 2

Distance of sncRNAs to the gene boundary (outside a start or stop codon).

Figure 3

Similarity clustering based on sequence identities of sncRNAs between CCEF00389 and seven other basidiomycetous fungi: (a) the hierarchical clustering tree; (b) the heat map of identities; the black color means no matches at the cutoff 1e − 3 (1e − 1 for miRNAs, because the length of their sequences is short).