| Shiitake mushroom (Lentinula edodes) is one of the most important cultivated mushrooms and wood-degrading fungi. To facilitate functional genomic analyses in the mushroom, the 39.8-Mb L. edodes genome was sequenced using multiple next-generation sequencing platforms. There are 5,116 simple sequence repeat loci and 13,382 predicted protein-coding genes. Among the genes, 36.5% are specific to L. edodes while 8.8% are conserved among mushrooms and absent in ascomycetes.;Comparative analyses revealed conserved genes in mushroom genomes, particularly putative regulators, protein-binding proteins and transcription factors. A mushroom-specific subunit (Csn8) of COP9 signalosome, which is associated with protein degradation, was also identified. Fruiting body development is potentially regulated by these conserved genes.;The unique composition of plant biomass-degrading enzymes in L. edodes genome was revealed. There are both laccases and peroxidases for lignin degradation. Multiple polysaccharide-degradation enzyme families were expanded, including glycoside hydrolase families 3 and 28 targeting beta-glycans and pectin, respectively.;Sequencing the A mating-type locus of 9 additional haploid strains discovered a total of six alleles. Two intron-Iength polymorphism markers were developed for PCR-based determination of A mating type. Surprisingly, L. edodes is the first known exception that mitochondrial intermediate peptidase gene is not directly linked to the A locus but located >47 kb away.;To facilitate computational analysis of mushroom genome sequences, Comparative Mushroom Genomics Platform was constructed using software packages Ensembl, GBrowse, BioMart, Galaxy and BLAST. Eight mushroom-forming basidiomycete genomes and 11 other fungal genomes were included. The platform is available through both web-based interactive access and programmatic access.;The L. edodes genome sequence, comparative genome analysis and computational analysis platform will serve as a key resource for the mushroom research community. |
