Lentinula edodes, has been utilized as food, as well as, in popular medicine, moreover, its extract isolated from its mycelium and fruiting body have shown several therapeutic properties. Yet little is understood about its genes involved in these properties, and the absence of L edodes genomes has been a barrier to the development of functional genomics research. However, high throughput sequencing technologies are now being widely applied to non-model species. To facilitate research on L edodes, we leveraged Solexa sequencing technology in de novo assembly of L edodes C91-3 transcriptome. In a single run, we produced more than 57 million sequencing reads. These reads were assembled into 28,923 unigene sequences (mean size = 689 bp) including 18,120 unigenes with coding sequence (CDS). Based on similarity search with known proteins, assembled unigene sequences were annotated with gene descriptions, gene ontology (GO) and clusters of orthologous group (COG) terms. Our data provides the first comprehensive sequence resource available for functional genomics studies in L edodes, and demonstrates the utility of Illumina/Solexa sequencing for de novo transcriptome characterization and gene discovery in a non-model mushroom. (C) 2012 Elsevier Inc. All rights reserved.