Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation

Abstract

Lentinula edodes, one of the most popular, edible mushroom species with a high content of proteins and polysaccharides as well as unique aroma, is widely cultivated in many Asian countries, especially in China, Japan and Korea. As a white rot fungus with lignocellulose degradation ability, L. edodes has the potential for application in the utilization of agriculture straw resources. Here, we report its 41.8-Mb genome, encoding 14,889 predicted genes. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of L. edodes and Gymnopus luxurians was estimated to be 39 MYA. The carbohydrate-active enzyme genes in L. edodes were compared with those of the other 25 fungal species, and 101 lignocellulolytic enzymes were identified in L. edodes, similar to other white rot fungi. Transcriptome analysis showed that the expression of genes encoding two cellulases and 16 transcription factor was up-regulated when mycelia were cultivated for 120 minutes in cellulose medium versus glucose medium. Our results will foster a better understanding of the molecular mechanism of lignocellulose degradation and provide the basis for partial replacement of wood sawdust with agricultural wastes in L. edodes cultivation.

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis

“…Lentinula edodes belongs to Marasmiaceae, which includes white rot, saprobic, and plant-pathogenic fungi (34). Plant cell wall-degrading enzymes in Lentinula edodes G408PP-4 (see Table S3) were identical to those of strain W1-26 (16) and similar to other species of Marasmiaceae (Table S3) (35)(36)(37). Characteristically, no lignin peroxidase (Lip)-encoding genes were found in Lentinula edodes or in Marasmiaceae species whose genome sequences are publicly available (Table S3), suggesting that Lentinula edodes lacks Lip and depends on laccases and manganese peroxidases for lignin degradation.…”

“…Because of the popularity of next-generation sequencing, many genome sequence drafts of basidiomycetous fungi are publicly available, especially from the 1,000 Fungal Genomes Project (14). More recently, the constructions of de novo draft genome sequences of Lentinula edodes were reported (15,16).…”

“…Transcriptome analyses for fruiting body development in Lentinula edodes were carried out using differential display (17) or serial analysis of gene expression (SAGE) analysis (18), and PCR subtraction was used for analyzing postharvest quality loss (19). More recently, transcriptome analysis was performed by transcriptome sequencing (RNA-seq) during browning film formation on mycelial bags (20) and during cellulose degradation (16). In Lentinula edodes, postharvest quality loss is a very significant problem from an economical viewpoint.…”

Proteome and Transcriptome Reveal Involvement of Heat Shock Proteins and Indoleacetic Acid Metabolism Process in Lentinula Edodes Thermotolerance

“…The indices were constructed via bowtie2 according to L. edodes genome files [35], followed by mapping RNA-seq reads to the L. edodes genome by tophat 2 using the default settings [36]. Subsequently, Samtools creates sam files for bam files [37].…”

“…In brief, peptide extract in 100% CAN and 0.5% trifluoroacetic acid was analyzed by LC-MS/MS using an LTQ-Orbitrap Velos mass spectrometer (Thermo Scientific) coupled to a nano Easy high-performance liquid chromatography equipment. Raw MS/MS data were searched against the genome of L. edodes v1.0 [35], using the search engine MaxQuant (version 3. 2.…”