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Background  The white-rot fungus  Phlebia  sp. MG-60 shows valuable properties such as high ethanol yield from several lignocellulosic materials, although white-rot fungi commonly degrade woody components to CO 2  and H 2 O. In order to identify genes involved in ethanol production by  Phlebia  sp. MG-60, we compared genes differentially expressed by the ethanol producing fungus  Phlebia  sp. MG-60 and the model white-rot fungus  Phanerochaete chrysosporium  under ethanol fermenting and non-fermenting conditions using next-generation sequencing technologies.    Results  mRNAs from mycelia of  Phlebia  sp. MG-60 and  P. chrysosporium  under fermenting and non-fermenting conditions were sequenced using the MiSeq system. To detect differentially expressed genes, expression levels were measured in fragments per kilobase of exon per million mapped reads (FPKM). Differentially expressed genes were annotated using BLAST searches, Gene Ontology classifications, and KEGG pathway analysis. Functional analyses of differentially expressed genes revealed that genes involved in glucose uptake, glycolysis, and ethanol synthesis were widely upregulated in  Phlebia  sp. MG-60 under fermenting conditions.    Conclusions  In this study, we provided novel transcriptomic information on  Phlebia  sp. MG-60, and these RNA-seq data were useful in targeting genes involved in ethanol production for future genetic engineering.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2977-7) contains supplementary material, which is available to authorized users.

Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq