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.

Fig 1. The ideogram showing the genomic features of Lentinula edodes.

(a) Scaffolds: the diagram represents 41 scaffolds of L. edodes, half of the genome size. (b) GC content was calculated as the percentage of G+C in 20-kb non-overlapping windows. (c) Gene number was calculated in 20-kb non-overlapping windows, and the maximum value of the axis is 15. (d) Gene expression of 2 samples with red (FPKM > = 100), orange (FPKM > = 10), green (FPKM > = 0) and black (FPKM = 0) colors. The out ring presents the gene expression of mycelia cultured by medium with cellulose as the main carbon source, and the inner ring presents the gene expression of mycelia cultured by medium with glucose as the main carbon source. (e) Large segmental duplications: regions sharing more than 90% sequence similarity are connected by orange (sequence length > = 5kb) and grey (sequence length > = 2kb) lines.

Fig 2. Orthologous gene number and phylogenetic tree of Lentinula edodes with other 25 fungal species.

(a) The topology of the phylogenetic tree was constructed by the maximum likelihood method (bootstrap = 1000, LG+I+G+F model), and all bootstrap values were 100%. Time scale was shown by MYA (million years ago). (b) Orthologous gene number was calculated in each fugal species at 26 different levels.

Fig 3. Distribution of genes in the matA and matB loci of Lentinula edodes strain W1-26.

The matA and matB loci are positioned on scaffold 1 and 53, respectively. We identified 3 additional pheromone receptor like genes on scaffold 6, 28, and 67.

Fig 4. Distribution of various glycoside hydrolases and carbohydrate binding module 1.

Lentinula edodes (out ring), Phanerochaete chrysosporium (second ring counted from out), Postia placenta (third ring) and Volvariella volvacea (inner ring).