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

Abstract

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.

Keywords: Cordyceps militaris; Entomopathogenic fungi; Genome; SMRT sequencing; Secondary metabolite.

Fig. 1

Phylogenetic tree showing evolutionary relationships between common fungal species and insect pathogenic species, including Cordyceps militaris, the species of interest in this study. Insect pathogenic fungi are highlighted by a blue box

Fig. 2

Comparison of mating type loci and surrounding genes in C. militaris ATCC® 34164 and C militaris Cm01. MAT 1-1-1 gene is shown in green, MAT 1-1-2 gene is shown in cyan, MAT 1-2-1 gene is shown in orange. Select genes are numbered for reference in the figure. Gene names from left to right are also listed in corresponding table. a C. militaris ATCC® 34164. b C. militaris Cm01. c Table of potential gene function and name

Fig. 3

Putative natural products in C. militaris. The classes of natural products are denoted by the following colors NRPS (cyan), T1PKS (orange), T1PKS-NRPS (red), Indole (indigo), Other (green) Terpene (violet). a The distribution of natural product producing gene clusters on the chromosomes of C. militaris. b The number of natural product gene cluster on each chromosome, grouped by class

Fig. 4

Comparison of gene clusters producing a 2-pyridone alkaloid molecule to the genes A9K55_001190 to A9K55_001192 in cluster III-1 in C. militaris ATCC ® 34164. The desmethylbassianin cluster (dmb), tenellin (ten), and fumosorone (fum) clusters are shown. Genes are color coded by function. Structures of 2-pyridone alkaloids are displayed

Fig. 5

Comparison of genes A9K55_005039, A9K55_005040, A9K55_005043 and A9K55_005044 in C. militaris ATCC® 34164 to an emericellamide producing gene cluster in Aspergillus nidulans. Genes are color coded by function. The structure of emericellamide is displayed

Fig. 6

Comparison of genes A9K55_008762 to A9K55_008769 in C. militaris ATCC® 34164 to an equisetin producing cluster in Fusarium heterosporum. Genes are color coded by function. The structure of equisetin is displayed