The ascomycete fungus Beauveria bassiana is a pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. We sequenced the genome of B. bassiana and a phylogenomic analysis confirmed that ascomycete entomopathogenicity is polyphyletic, but also revealed convergent evolution to insect pathogenicity. We also found many species-specific virulence genes and gene family expansions and contractions that correlate with host ranges and pathogenic strategies. These include B. bassiana having many more bacterial-like toxins (suggesting an unsuspected potential for oral toxicity) and effector-type proteins. The genome also revealed that B. bassiana resembles the closely related Cordyceps militaris in being heterothallic, although its sexual stage is rarely observed. A high throughput RNA-seq transcriptomic analysis revealed that B. bassiana could sense and adapt to different environmental niches by activating well-defined gene sets. The information from this study will facilitate further development of B. bassiana as a cost-effective mycoinsecticide.

Metarhizium spp. are being used as environmentally friendly alternatives to chemical insecticides, as model systems for studying insect-fungus interactions, and as a resource of genes for biotechnology. We present a comparative analysis of the genome sequences of the broad-spectrum insect pathogen Metarhizium anisopliae and the acridid-specific M. acridum. Whole-genome analyses indicate that the genome structures of these two species are highly syntenic and suggest that the genus Metarhizium evolved from plant endophytes or pathogens. Both M. anisopliae and M. acridum have a strikingly larger proportion of genes encoding secreted proteins than other fungi, while ∼30% of these have no functionally characterized homologs, suggesting hitherto unsuspected interactions between fungal pathogens and insects. The analysis of transposase genes provided evidence of repeat-induced point mutations occurring in M. acridum but not in M. anisopliae. With the help of pathogen-host interaction gene database, ∼16% of Metarhizium genes were identified that are similar to experimentally verified genes involved in pathogenicity in other fungi, particularly plant pathogens. However, relative to M. acridum, M. anisopliae has evolved with many expanded gene families of proteases, chitinases, cytochrome P450s, polyketide synthases, and nonribosomal peptide synthetases for cuticle-degradation, detoxification, and toxin biosynthesis that may facilitate its ability to adapt to heterogenous environments. Transcriptional analysis of both fungi during early infection processes provided further insights into the genes and pathways involved in infectivity and specificity. Of particular note, M. acridum transcribed distinct G-protein coupled receptors on cuticles from locusts (the natural hosts) and cockroaches, whereas M. anisopliae transcribed the same receptor on both hosts. This study will facilitate the identification of virulence genes and the development of improved biocontrol strains with customized properties. Aside from playing a crucial role in natural ecosystems, entomopathogenic fungi are being developed as environmentally friendly alternatives for the control of insect pests. We conducted the first genomic study of two of the best characterized entomopathogens, Metarhizium anisopliae and M. acridum. M. anisopliae is a ubiquitous pathogen of >200 insect species and a plant growth promoting colonizer of rhizospheres. M. acridum is a specific pathogen of locusts. Important findings of this study included: 1) Both M. anisopliae and M. acridum have a very large number of genes encoding secreted proteins, and many of these play roles in fungus-insect interactions. 2) M. anisopliae has more genes than M. acridum, which may be associated with adaptation to multiple insect hosts. 3) Unlike M. acridum, the M. anisopliae genome contains many more transposase genes and shows no evidence of repeat-induced point mutations. The lack of repeat-induced mutations may have allowed the lineage-specific gene duplications that have contributed to its adaptability. 4) High-throughput transcriptomics identified the strategies by which these fungi overcome their insect hosts and achieve specificity. These genome sequences will provide the basis for a comprehensive understanding of fungal–plant–insect interactions and will contribute to our understanding of fungal evolution and ecology.

Background: Species in the ascomycete fungal genus Cordyceps have been proposed to be the teleomorphs of Metarhizium species. The latter have been widely used as insect biocontrol agents. Cordyceps species are highly prized for use in traditional Chinese medicines, but the genes responsible for biosynthesis of bioactive components, insect pathogenicity and the control of sexuality and fruiting have not been determined. Results: Here, we report the genome sequence of the type species Cordyceps militaris. Phylogenomic analysis suggests that different species in the Cordyceps/Metarhizium genera have evolved into insect pathogens independently of each other, and that their similar large secretomes and gene family expansions are due to convergent evolution. However, relative to other fungi, including Metarhizium spp., many protein families are reduced in C. militaris, which suggests a more restricted ecology. Consistent with its long track record of safe usage as a medicine, the Cordyceps genome does not contain genes for known human mycotoxins. We establish that C. militaris is sexually heterothallic but, very unusually, fruiting can occur without an opposite mating-type partner. Transcriptional profiling indicates that fruiting involves induction of the Zn2Cys6-type transcription factors and MAPK pathway; unlike other fungi, however, the PKA pathway is not activated. Conclusions: The data offer a better understanding of Cordyceps biology and will facilitate the exploitation of medicinal compounds produced by the fungus.

Significance: Fossil records have provided compelling evidence for evolution, but lack of existing transitional species has hindered our understanding of speciation at the molecular level. Genomic analyses of seven Metarhizium species revealed a directional speciation continuum from specialists with narrow host ranges to transitional species and then to generalists that paralleled insect evolution. This diversification was coupled with a complex interplay between an array of genomic features that worked together to drive fungal speciation at an accelerating rate and provided a roadmap for identifying variation underlying adaptation and speciation. In particular, specialization was associated with retention of sexuality and rapid evolution of existing protein sequences whereas generalization was associated with loss of sexuality and protein-family expansion.

Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens; however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen–host cospeciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus–animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation.

The caterpillar fungus Ophiocordyceps sinensis (best known as Cordyceps sinensis) mummifies ghost moth larvae exclusively in Tibetan Plateau alpine ecosystems. Touted as “Himalayan Viagra”, the fungus is highly prized due to its medical benefits and dwindling supplies. Attempts to culture the sexual fruiting-body have failed and the huge market demand has led to severe devastation of local ecosystems and to the fungus heading towards extinction. By genome sequencing, we establish that unlike related insect pathogens O. sinensis contains two compatible mating-type genes in its genome and is self-fertile, i.e. homothallic. However, sexual processes are only initiated under native environmental conditions. O. sinensis resembles biotrophic plant pathogens in having a genome shaped by retrotransposon-driven expansions. The resulting changes in gene content suggest that O. sinensis has a biphasic pathogenic mechanism beginning with stealth pathogenesis in early host instars. O. sinensis is the first psychrophilic fungus sequenced and is adapted to extreme cold with putative antifreeze proteins and mechanisms for increasing lipid accumulation and fatty acid unsaturation. We hypothesize that for the inbreeding O. sinensis the massive proliferation of retrotransposons provides a tradeoff between the advantages of increased genetic variation independent of sexual recombination and deletion of genes dispensable for its specialized pathogenic lifestyle.