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Background  Ascomycete  Cordyceps  species have been using as valued traditional Chinese medicines. Particularly, the fruiting bodies of  Cordyceps cicadae  (syn.  Isaria cicadae ) have long been utilized for the treatment of chronic kidney disease. However, the genetics and bioactive chemicals in this fungus have been largely unexplored.    Results  In this study, we performed comprehensive omics analyses of  C. cicadae , and found that, in contrast to other  Cordyceps  fungi,  C. cicadae  produces asexual fruiting bodies with the production of conidial spores instead of the meiotic ascospores. Genome sequencing and comparative genomic analysis indicate that the protein families encoded by  C. cicadae  are typical of entomopathogenic fungi, including the expansion of proteases and chitinases for targeting insect hosts. Interestingly, we found that the MAT1-2 mating-type locus of the sequenced strain contains an abnormally truncated  MAT1-1-1  gene. Gene deletions revealed that asexual fruiting of  C. cicadae  is independent of the MAT locus control. RNA-seq transcriptome data also indicate that, compared to growth in a liquid culture, the putative genes involved in mating and meiosis processes were not up-regulated during fungal fruiting, further supporting asexual reproduction in this fungus. The genome of  C. cicadae  encodes an array of conservative and divergent gene clusters for secondary metabolisms. Based on our analysis, the production of known carcinogenic metabolites by this fungus could be potentially precluded. However, the confirmed production of oosporein raises health concerns about the frequent consumption of fungal fruiting bodies.    Conclusions  The results of this study expand our knowledge of fungal genetics that asexual fruiting can occur independent of the MAT locus control. The obtained genomic and metabolomic data will benefit future investigations of this fungus for medicinal uses.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-4060-4) contains supplementary material, which is available to authorized users.

Omics data reveal the unusual asexual-fruiting nature and secondary metabolic potentials of the medicinal fungus Cordyceps cicadae