Identification of Long Non-Coding RNAs and Their Target Genes from Mycelium and Primordium in Model Mushroom Schizophyllum commune.

Schizophyllum commune has emerged as the most promising model mushroom to study developmental stages (mycelium, primordium), which are two primary processes of fruit body development. Long non-coding RNA (lncRNA) has been proved to participate in fruit development and sex differentiation in fungi. However, potential lncRNAs have not been identified in S. commune from mycelium to primordium developmental stages. In this study, lncRNA-seq was performed in S. commune and 61.56 Gb clean data were generated from mycelium and primordium developmental stages. Furthermore, 191 lncRNAs had been obtained and a total of 49 lncRNAs were classified as differently expressed lncRNAs. Additionally, 26 up-regulated differently expressed lncRNAs and 23 down-regulated between mycelium and primordia libraries were detected. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed lncRNAs target genes from the MAPK pathway, phosphatidylinositol signal, ubiquitin-mediated proteolysis, autophagy, and cell cycle. This study provides a new resource for further research on the relationship between lncRNA and two developmental stages (mycelium, primordium) in S. commune.

Whole-Genome Sequencing and Transcriptome Analysis of Ganoderma lucidum Strain Yw-1-5 Provides New Insights into the Enhanced Effect of Tween80 on Exopolysaccharide Production.

Ganoderma lucidum is an important medicinal mushroom widely cultured in Asian countries. Exopolysaccharides are bioactive compounds of G. lucidum with health benefits. Limited exopolysaccharide content hinders its extraction from G. lucidum. The addition of Tween80 had an enhanced effect on G. lucidum exopolysaccharide production in submerged fermentation. However, the mechanism of this effect remains unclear. In this study, we report on a high-quality assembly of G. lucidum strain yw-1-5 to lay the foundation for further transcriptome analysis. The genome sequence was 58.16 Mb and consisted of 58 scaffolds with an N50 of 4.78 Mb. A total of 13,957 protein-coding genes were annotated and Hi-C data mapped to 12 pseudo-chromosomes. Genes encoding glycosyltransferases and glycoside hydrolases were also obtained. Furthermore, RNA-seq was performed in a Tween80-treated group and control group for revealing the enhanced effect of Tween80 on exopolysaccharide production. In total, 655 genes were identified as differentially expressed, including 341 up-regulated and 314 down-regulated. Further analysis of differentially expressed genes showed that groups of MAPK, amino sugar and nucleotide sugar metabolism, autophagy, ubiquitin-mediated proteolysis, peroxisome, starch and sucrose metabolism, TCA cycle, glycolysis/gluconeogenesis KEGG pathway, glycosyltransferases and glycoside hydrolases played important roles in the enhanced effect of Tween80 on exopolysaccharide production. This work provides a valuable resource for facilitating our understanding of the synthesis of polysaccharides and accelerating the breeding of new strains with a high content of exopolysaccharides.

De novo transcriptome sequencing of Flammulina velutipes uncover candidate genes associated with cold-induced fruiting.

To understand molecular mechanism of cold-induced fruiting in Flammulina velutipes, which is one of most popular edible fungi in east Asia, de novo assembly of the F. velutipes transcriptome was carried out. There were 26,888,494 and 26,275,146 clean reads obtained from mycelium and primordia of F. velutipes, respectively. A total of 20,157 unigenes were de novo assembled and 15,058 of them were annotated. Moreover, 7935 unigenes were differentially expressed between mycelium and primordia, 4025 of them were up-regulated and 3910 were down-regulated. GO and KEGG pathway analysis of the differentially expressed unigenes indicated that functional groups associated with two-component signaling pathway, calcium signaling, mitogen-actived protein kinase pathway, molecular chaperones, cell wall and membrane system, play an important role in cold-induced fruiting of F. velutipes. In this work 643 EST-SSRs were identified in 20,157 unigenes and 1560 EST-SSRs primers pairs were designed. Moreover, 5548 and 5955 SNPs were detected in mycelium and primordia, respectively. Consequently, results of this work can serve as a valuable resource for functional genomics study of cold-induced fruiting in F. velutipes.