Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Abstract

Background: Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. To understand the molecular mechanisms underlying this critical developmental process in L. edodes, we characterized the morphological phenotypic changes in a strain, Chamaram, associated with abnormal brown film formation and compared its genome-wide transcriptional features.

Results: In the present study, we performed genome-wide transcriptome analyses of different vegetative mycelium growth phenotypes, namely, early white, normal brown, and defective dark yellow partial brown films phenotypes which were exposed to different light conditions. The analysis revealed the identification of clusters of genes specific to the light-induced brown film phenotypes. These genes were significantly associated with light sensing via photoreceptors such as FMN- and FAD-bindings, signal transduction by kinases and GPCRs, melanogenesis via activation of tyrosinases, and cell wall degradation by glucanases, chitinases, and laccases, which suggests these processes are involved in the formation of mycelial browning in L. edodes. Interestingly, hydrophobin genes such as SC1 and SC3 exhibited divergent expression levels in the normal and abnormal brown mycelial films, indicating the ability of these genes to act in fruiting body initiation and formation of dikaryotic mycelia. Furthermore, we identified the up-regulation of glycoside hydrolase domain-containing genes in the normal brown film but not in the abnormal film phenotype, suggesting that cell wall degradation in the normal brown film phenotype is crucial in the developmental processes related to the initiation and formation of fruiting bodies.

Conclusions: This study systematically analysed the expression patterns of light-induced browning-related genes in L. edodes. Our findings provide information for further investigations of browning formation mechanisms in L. edodes and a foundation for future L. edodes breeding.

Keywords: Brown film; Cell wall degradation; Fruit body; Lentinula edodes; Light sensing; Mycelium; Transcriptome.

Fig. 1

Brown film formation and fruit body development in the sawdust cultivation of the Lentinula edodes strain Chamaram. a Light-induced brown film formation on sawdust media. b Development of L. edodes fruiting bodies. c Fruiting body development and contamination by Trichoderma sp. on normal and dark yellow films formed by mycelial tissues. d Microstructures of white (W), normal brown (B), and partial brown (BP) film mycelium

Fig. 2

Overview of differential expression analysis for white (W), normal brown (B), and partial brown (BP) film mycelium. a Pearson correlation coefficients for pair-wise comparisons of the W, B, and BP mycelium transcriptome data. b Number of up- and down-regulated genes. c Gene set enrichment analysis (GSEA) of differentially expressed genes

Fig. 3

Light-induced phenotype-specific clusters and their functions. a Venn diagram presenting the overlap of differentially expressed genes among the three comparisons (W vs B, W vs BP, and B vs BP). b Hierarchical clustering heatmap of gene expression for each cluster and the representative gene ontology (GO) terms. The GO terms were analysed by GSEA (P < 0.01). Expression values (FPKMs) of genes were transformed to Z-score values.

Fig. 4

Genes involved in the regulation of mycelial browning in Lentinula edodes. The right side of the heatmap indicates the ID of the gene model of L. edodes and the homologous gene name. The gene expression values (FPKMs) were transformed to Z-score values

Fig. 5

The distribution of carbohydrate-active enzyme-encoding genes identified from the differentially expressed gene sets (a) and the expression heatmap of these genes (b). The corresponding genes were searched using the carbohydrate-active enzyme database (CAZy) and were classified into primary domains such as glycoside hydrolase (GH), auxiliary activity (AA), carbohydrate-binding module (CBM), carbohydrate esterase (CE), glycosyl transferase (GT), and polysaccharide lyase (PL)

Fig. 6

Gene expression changes in starch (a) and sucrose (b) metabolism