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Background    Cordyceps militaris  is an insect pathogenic fungus that is prized for its use in traditional medicine. This and other entomopathogenic fungi are understudied sources for the discovery of new bioactive molecules. In this study, PacBio SMRT long read sequencing technology was used to sequence the genome of  C. militaris  with a focus on the genetic potential for secondary metabolite production in the genome assembly of this fungus.    Results  This is first chromosome level assembly of a species in the  Cordyceps  genera. In this seven chromosome assembly of 33.6 Mba there were 9371 genes identified.  Cordyceps militaris  was determined to have the MAT 1-1-1 and MAT 1-1-2 mating type genes. Secondary metabolite analysis revealed the potential for at least 36 distinct metabolites from a variety of classes. Three of these gene clusters had homology with clusters producing desmethylbassianin, equisetin and emericellamide that had been studied in other fungi.    Conclusion  Our assembly and analysis has revealed that  C. militaris  has a wealth of gene clusters for secondary metabolite production distributed among seven chromosomes. The identification of these gene clusters will facilitate the future study and identification of the secondary metabolites produced by this entomopathogenic fungus.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-4307-0) contains supplementary material, which is available to authorized users.

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris