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.
Highlights
Basidiomycetous fungus Lentinula edodes, the shiitake mushroom, is the second most popular edible and medicinal mushroom in terms of total global output and economic value in East Asia[1,2]
To identify transcriptomic changes in two developmental stages of the commercially important Korean L. edodes strain Sanjo[701] (SJ701)[3,4], high-throughput sequencing in RNA samples extracted from L. edodes dikaryotic mycelia and mature fruiting bodies was the first performed using Illumina paired-end sequencing technology according to the transcriptome analysis workflow (Fig. 1)
27,646,278 and 30,109,768 clean paired-end sequence reads were obtained from the mycelium and mature fruiting body, respectively, with a Q20 percentage >72.2%, using the DynamicTrim and LengthSort programs[30]
Summary
Basidiomycetous fungus Lentinula edodes, the shiitake mushroom, is the second most popular edible and medicinal mushroom in terms of total global output and economic value in East Asia[1,2]. To analyze differentially expressed genes (DEGs) between two major developmental stages (i.e., mycelium and fruiting body), high-throughput sequencing has been used for genome and transcriptome analyses of basidiomycota mushrooms, including Agrocybe aegerita, Auricularia polytricha, Cordyceps militaris, and Ganoderma lucidum. There have been no transcription-level, genome-wide comparative studies of the development stages of mycelia and mature fruiting bodies of L. edodes commercial strains and their relation to yield. Despite the great importance of investigating the specific stages for the optimal production of beneficial nutritional and medicinal properties and the generation of improved L. edodes cultivars, the transcriptomes of dikaryotic mycelia and mature fruiting bodies of this species remain poorly understood. We performed the first comparative transcriptome analysis of two developmental stages, the mycelium and mature fruiting body
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