Dataset Information

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.

SUBMITTER: Qu J

PROVIDER: S-EPMC5040776 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus <i>Pleurotus ostreatus</i>.

Qu Jibin J Zhao Mengran M Hsiang Tom T Feng Xiaoxing X Zhang Jinxia J Huang Chenyang C

BioMed research international 20160915

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 <i>Pleurotus ostreatus</i>, 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 ba ...[more]

PMID: 27703969

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Project description:The edible oyster mushroom Pleurotus ostreatus is one of the most cultivated species worldwide. Morphogenesis associated with the maturation of fruit bodies is controlled by two unlinked loci of sexual compatibility matA and matB with multiple alleles (tetrapolar system of sexual compatibility). Quantitative analysis of the alleles of mating compatibility loci in 17 natural isolates collected in the Moscow region was performed in mon-mon (monokaryons-monokaryon) and di-mon (dikaryon-monokaryon) crossings. Four monokaryotic testers strains which were heteroallelic at both mating type loci were obtained for each of the five natural mushroom isolates by using original technique of sterile spore prints on Petri dishes and mon-mon crossing. Twelve natural isolates were crossed via di-mon mating with the four monokaryotic testers M-38. Genetic analysis of the alleles of sexual compatibility loci in 17 natural isolates revealed multiple alleles at both loci: at least ten alleles at matA locus and eight alleles at matB locus. Structural organization analysis of the matA locus was performed in silico for homokaryotic strains PC9 and PC15 based on the whole-genome sequencing data available at DOE Joint Genome Institute. The matA locus has an extremely divergent structure: there are one copy of the homeodomain gene hd1 and one copy of the hd2 gene in the PC9 strain, whereas the matA locus of the PC15 strain is composed by two copies of hd1.1 and hd1.2 genes (class HD1 homeodomain proteins) and one copy of hd2 gene (class HD2 proteins). Comprehensive analysis of amino acid sequences of HD1 and HD2 homeodomain proteins demonstrated that the proteins have a globular structure with the nuclear localization and contain a variable N-terminus and a more conserved DNA-binding domain with a specific conserved motif WFXNXR in the third ɑ-helix. The results suggest that multiple alleles of the matA locus of sexual compatibility in basidiomycete fungi is achieved due to both different copy number of the coding hd genes within the locus and the variability of the coding gene sequences.

Project description:The function of small secreted proteins (SSPs) in saprotrophic fungi is, for the most part, unknown. The white-rot mushroom Pleurotus ostreatus produces considerable amounts of SSPs at the onset of secondary metabolism, during colony development, and in response to chemical compounds such as 5-hydroxymethylfurfural and aryl alcohols. Genetic manipulation of Ssp1, by knockdown (KDssp1) or overexpression (OEssp1), indicated that they are, in fact, involved in the regulation of the ligninolytic system. To elucidate their potential involvement in fungal development, quantitative secretome analysis was performed during the trophophase and the idiophase and at a transition point between the two growth phases. The mutations conferred a time shift in the secretion and expression patterns: OEssp1 preceded the entrance to idiophase and secondary metabolism, while KDssp1 was delayed. This was also correlated with expression patterns of selected genes. The KDssp1 colony aged at a slower pace, accompanied by a slower decline in biomass over time. In contrast, the OEssp1 strain exhibited severe lysis and aging of the colony at the same time point. These phenomena were accompanied by variations in yellow pigment production, characteristic of entrance of the wild type into idiophase. The pigment was produced earlier and in a larger amount in the OEssp1 strain and was absent from the KDssp1 strain. Furthermore, the dikaryon harboring OEssp1 exhibited a delay in the initiation of fruiting body formation as well as earlier aging. We propose that Ssp1 might function as a part of the fungal communication network and regulate the pattern of fungal development and metabolism in P. ostreatusIMPORTANCE Small secreted proteins (SSPs) are common in fungal saprotrophs, but their roles remain elusive. As such, they comprise part of a gene pool which may be involved in governing fungal lifestyles not limited to symbiosis and pathogenicity, in which they are commonly referred to as "effectors." We propose that Ssp1 in the white-rot fungus Pleurotus ostreatus regulates the transition from primary to secondary metabolism, development, aging, and fruiting body initiation. Our observations uncover a novel regulatory role of effector-like SSPs in a saprotroph, suggesting that they may act in fungal communication as well as in response to environmental cues. The presence of Ssp1 homologues in other fungal species supports a common potential role in environmental sensing and fungal development.

Dataset Information

Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.

Publications

Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus <i>Pleurotus ostreatus</i>.

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