Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes

Abstract

Lentinula edodes is a popular cultivated edible mushroom with high nutritional and medicinal value. To understand the regulation of gene expression in the dikaryotic mycelium and mature fruiting body in the commercially important Korean L. edodes strain, we first performed comparative transcriptomic analysis, using Illumina HiSeq platform. De novo assembly of these sequences revealed 11,675 representative transcripts in two different stages of L. edodes. A total of 9,092 unigenes were annotated and subjected to Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Gene expression analysis revealed that 2,080 genes were differentially expressed, with 1,503 and 577 upregulated in the mycelium and a mature fruiting body, respectively. Analysis of 18 KEGG categories indicated that fruiting body-specific transcripts were significantly enriched in ‘replication and repair’ and ‘transcription’ pathways, which are important for premeiotic replication, karyogamy, and meiosis during maturation. We also searched for fruiting body-specific proteins such as aspartic protease, gamma-glutamyl transpeptidase, and cyclohexanone monooxygenase, which are involved in fruiting body maturation and isolation of functional substances. These transcriptomes will be useful in elucidating the molecular mechanisms of mature fruiting body development and beneficial properties, and contribute to the characterization of novel genes in L. edodes.

Comparative genomics reveals unique wood‐decay strategies and fruiting body development in the Schizophyllaceae

“…Of the fungal cell wall (FCW) associated genes, hydrophobins were mostly developmentally regulated (eight of 11 genes) in A. ampla (Fig. S3), often with significantly increased expression coincident with the transition from vegetative mycelium to Stage 1 primordia (in six genes), as observed previously (van Wetter et al ., , ; Banerjee et al ., ; Ohm et al ., ; Song et al ., ). Several members of two functionally similar families, cerato‐platanins (4 of 5 genes dev.…”

“…These genes showed 254‐ and 855‐fold upregulation in Stage 1 primordia of both A. ampla and S. commune , respectively, and had high expression in all fruiting body tissues (> 5000 FPKM, maximum fold change within fruiting bodies 3.4–3.7), suggesting an important role of heat shock proteins during fruiting body development. In further support of this hypothesis, homologs of these genes were found to be developmentally regulated or differentially expressed also in Laccaria bicolor fruiting bodies (Martin et al ., ), Lentinula edodes (Song et al ., ) , Armillaria ostoyae, Coprinopsis cinerea, Lentinus tigrinus and Rickenella mellea (Krizsán et al ., ). Another co‐ortholog with significant upregulation in Stage 1 primordia included A1 aspartic proteases, although the expression dynamics were somewhat different in the two species.…”

“…An induction in stage 1 primordia was observed in both, but, whereas upregulation in A. ampla was > 2009 compared to VM, it was only 149 in S. commune. Aspartic proteases of the A1 family have been reported as highly induced in fruiting bodies in several previous studies (Martin et al, 2008;Sabotic et al, 2009;Rahmad et al, 2014;Song et al, 2018;Krizs an et al, 2019), but no mechanistic hypothesis for their role in fruiting bodies has yet been proposed.…”

Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia

“…When combined with the results of the KEGG pathway analysis of the DEGs, this indicated that functional groups were associated with vitamin B6 metabolism, glycine metabolism, and cystathionine lyase, which might play an important role in LIPF in S. latifolia. Metabolism of vitamins was also involved in fruiting body formation in Lentinula edodes [37].…”

The PoV mycovirus affects extracellular enzyme expression and fruiting body yield in the oyster mushroom, Pleurotus ostreatus

“…SYBR green-based qRT-PCR was performed using FastStart Essential DNA Green Master mix (Roche, Basel, Switzerland) on a LightCycler 96 system (Roche). Statistical analysis of viral gene expression were calculated via the comparative threshold cycle method using the LightCycler 96 qualitative detection module (Roche), as described previously 42 . In addition, relative gene expression levels of target genes in the mycelia, fruiting bodies, and sawdust spawn were performed with the same qRT-PCR method for the viral gene.…”