In the world of biological pest control, few organisms are as commercially important as the entomopathogenic fungi of the genus Beauveria. These soilborne parasites, which infect insects through their cuticle and have been formulated as biopesticides for decades, include both broad-spectrum generalists and narrow specialists whose contrasting ecological strategies have long puzzled mycologists and applied entomologists alike. A new comparative genomic study published in Molecular Genetics and Genomics has now dissected, at the level of individual gene families, the molecular basis of that divergence — and the answer is more subtle than a wholesale rewiring of pathogenic machinery.
The research team, led by Alexandra M. Kortsinoglou and Vassili N. Kouvelis of the National and Kapodistrian University of Athens together with collaborators from Austria and Switzerland, focused on two commercially exploited species with fundamentally different lifestyles. Beauveria bassiana is a cosmopolitan generalist with a global distribution, capable of infecting economically important pests across multiple insect orders — thrips, whiteflies, spider mites and aphids among them — and frequently recovered as an endophyte or epiphyte living inside plant tissues, where it promotes growth and shields crops from disease. Beauveria brongniartii, by contrast, is a specialist whose virulence is aimed chiefly at soil-dwelling beetle larvae, most notably the European cockchafer Melolontha melolontha, a destructive scarab pest of central European agriculture, with only limited evidence that it can colonize plants.
To find the genomic signatures of this ecological split, the researchers sequenced the genome of the commercial B. brongniartii strain BIPESCO2, originally isolated from a cockchafer in Austria, and that of B. bassiana strain ATHUM 4946, retrieved from air samples in Athens. Sequencing was performed on the Oxford Nanopore MinION platform — using the higher-accuracy R10.4.1 flow cell chemistry for BIPESCO2 and R9.4.1 for ATHUM 4946 — with basecalling handled by Guppy’s super-accurate model. The resulting long reads were assembled de novo with Flye, polished through successive rounds with Racon and Medaka for BIPESCO2 and corrected with Canu for the B. bassiana strain, and annotated through the GenSAS v6.0 pipeline, which combined ab initio predictions from Augustus and GeneMark-ES with protein and transcript alignments to build consensus gene sets.
The quality of the resulting assemblies matters, because B. brongniartii has long suffered from fragmented genomic references. The BIPESCO2 assembly came out at 34.2 megabases in just ten contigs, with a contiguity N50 of 1.95 megabases and a longest contig of 3.69 megabases — figures comparable to reference-grade Beauveria genomes. Independent quality checks were rigorous: Inspector found no structural errors such as inversions, collapses or misjoins; 99.96 percent of reads mapped back to the assembly; and the estimated consensus accuracy of 99.99 percent (quality value 40.6) came at a mean sequencing depth of 124-fold. The official protein set scored 98 percent completeness against the Hypocreales BUSCO lineage dataset. The B. bassiana ATHUM 4946 assembly, at 34.7 megabases across 11 contigs with an N50 of 4 megabases, reached 95.7 percent BUSCO completeness. Both assemblies were deposited in the European Nucleotide Archive.
Armed with these reference-quality genomes, the team widened the lens to 20 genomes in total — 18 B. bassiana strains selected from 206 publicly available assemblies based on contiguity thresholds, plus two B. brongniartii strains — and carried out genome-wide orthology inference. Nearly all genes, 200,848 of them, sorted into 11,642 orthogroups, and the core genome proved vast: 8,032 orthogroups contained representatives from every strain, and 7,425 of those were strictly single-copy. Phylogenetic analysis of single-copy orthologues, rooted with two Cordyceps outgroups, cleanly separated the two species into distinct, well-supported clades. Applying a strict specificity criterion — a gene family present in all strains of one species and absent from all strains of the other — the researchers identified 201 B. bassiana-specific and 244 B. brongniartii-specific orthogroups. Notably, these lineage-restricted families were heavily divergent at the sequence level, with large fractions lacking recognizable conserved domains altogether, a hallmark of rapid evolution at host-interaction loci.
The functional flavor of those species-specific genes was telling. In B. bassiana, the generalist, the unique repertoire leaned toward broad metabolic versatility and stress tolerance: protein-binding domains, transmembrane transporters, monooxygenases and oxidoreductases, protein kinases, and a mix of peptidases including M35 deuterolysins and M60 metalloproteases capable of breaching the insect peritrophic membrane. There were also expanded multidrug-efflux transporter families of the MFS class, detoxification systems, and — strikingly — a single-copy orthologue encoding a Delta-endotoxin CytB-like protein, homologous to the pore-forming toxins of Bacillus thuringiensis. B. brongniartii, meanwhile, carried a narrower but more specialized toolkit: FAD-dependent oxidoreductases, O-methyltransferases, chitin- and carbohydrate-binding modules such as LysM and CFEM, an Egh16-like domain known from appressorium-specific virulence in plant pathogens, Tryp_SPc serine proteases targeting the cuticle, and a wide range of nutrient, ion and heavy-metal efflux transporters. Among its unique genes were an Rhs-associated toxin module previously known mainly from Gram-negative bacteria, an enterotoxin-like protein shared with Cordyceps militaris, and a polyketide synthase found so far only in one C. militaris strain.
Carbohydrate-active enzymes told a different story — one of remarkable conservation. Across all 20 genomes, 150 CAZyme families were shared, with minimal differences in copy number, indicating that both the generalist and the specialist retain a versatile enzymatic toolkit suitable for plant association, saprotrophy on dead organic matter, and insect pathogenicity alike. The chitin-cutting GH18 family, essential for degrading the insect cuticle, was the most expanded, with 271 proteins across the dataset, each strain carrying 13 or 14 copies, often decorated with chitin-binding CBM18, CBM1 or LysM modules that enhance substrate recognition and may help shield the pathogen from host immune detection. Chitin deacetylases that convert chitin to less recognizable chitosan were universally present. Yet within the conserved backdrop, a few families varied consistently between species: B. brongniartii possessed an extra GH27 α-galactosidase lacking the CBM13 binding domain found in its fused counterparts, more copies of AA7 flavin-dependent oxidases, and — uniquely among all Beauveria genomes examined — a PL20 polysaccharide lyase family encoding alginate and uronate-cleaving enzymes, hinting at a distinct substrate niche.
The sharpest species-level differences emerged in secondary metabolism. Each Beauveria genome carries on average around 46 biosynthetic gene clusters, and network analysis grouped the 922 clusters across the dataset into 105 gene cluster families, of which 25 formed the genus-wide core — including the genes for the insecticidal cyclodepsipeptides bassianolide and beauverolide, the antimicrobial pigment oosporein, and several siderophores. But on top of that shared core, B. brongniartii had expanded its arsenal of type I polyketide synthase clusters, with 11 copies compared to 6 to 9 in B. bassiana, and harbored six species-specific clusters, mostly predicting novel, heavily oxygenated polyketides, plus a terpene cluster complete with a squalene synthase and tailoring machinery. Even more intriguing were the structural remodelings of shared virulence clusters. In the beauverolide cluster, B. brongniartii has lost the phenylalanine-specific adenylation domain and the terminal D-isoleucine module of its nonribosomal peptide synthetase, and has swapped the Fe(II)-dependent hydroxylase of B. bassiana for an N-monooxygenase — a coordinated enzymatic substitution predicted to yield less hydroxylated, more hydrophobic beauverolide analogues. The bassianolide cluster, too, showed extensive rearrangement of tailoring enzymes between the two lineages, and the beauvericin cluster, intact in B. bassiana, exists in B. brongniartii only in truncated, likely nonfunctional form.
Effector proteins — secreted molecules that modulate host immunity — followed the same pattern of a conserved core with lineage-specific embellishments. Using signal peptide prediction, transmembrane filtering and EffectorP v3.0, the researchers identified an average of 336 candidate effectors per strain, the majority apoplastic. Orthology analysis condensed 6,330 effector proteins into 455 orthogroups, with 130 core effector families shared across the genus and only 17 strictly conserved in every strain, most of them of unknown function. The species-specific effector sets were enriched in adhesion, immunity and cuticle-interaction domains, and many B. brongniartii effectors matched experimentally validated virulence proteins from plant pathogens such as Magnaporthe oryzae, Colletotrichum gloeosporioides and Fusarium solani — evidence of convergent or repurposed virulence mechanisms spanning ecological boundaries.
Taken together, the study paints a picture in which host-range divergence in Beauveria is not achieved by discarding the core infection machinery — adhesion, germination, penetration, hemocoel proliferation — which remains largely intact and conserved. Instead, the specialist and the generalist differ in a compartmentalized set of genomic compartments: the secondary metabolite clusters that shape the chemical weapons deployed during infection, and a limited subset of lineage-restricted virulence factors governing surface interaction and immune evasion. The improved BIPESCO2 reference genome now gives researchers working on cockchafer biocontrol a solid genomic scaffold, while the identification of species-specific polyketide pathways and remodeled cyclodepsipeptide clusters offers a rich vein of unexplored chemistry — compounds whose biological roles, from insecticidal synergy to antimicrobial defense, now await experimental confirmation. For a genus upon which agriculture increasingly relies as synthetic pesticides face mounting restrictions, knowing exactly where the genetic levers of host specificity reside is a practical step toward designing more targeted, more predictable biological control agents.
Subject of Research: Comparative genomics of the generalist entomopathogenic fungus Beauveria bassiana and the specialist Beauveria brongniartii, identifying genomic signatures of host-range divergence.
Subject of Research: Biology
Article Title: Genomic signatures of host-range divergence in the generalist Beauveria bassiana and the specialist Beauveria brongniartii
Article References: Kortsinoglou, A. M., Popp-Embleton, H., Enkerli, J., Strasser, H., & Kouvelis, V. N. (2026). Genomic signatures of host-range divergence in the generalist Beauveria bassiana and the specialist Beauveria brongniartii. Molecular Genetics and Genomics, 301(1), Article 192. https://doi.org/10.1007/s00438-026-02506-z
Image Credits: AI Generated
DOI: 10.1007/s00438-026-02506-z
Keywords: Beauveria bassiana, Beauveria brongniartii, entomopathogenic fungi, host range, comparative genomics, biosynthetic gene clusters, effectors, CAZymes, biological control
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Gavin Prescott. (September 11, 2026). Host-range evolution revealed in Beauveria bassiana and Beauveria brongniartii genomes. Scienmag. https://scienmag.com/host-range-evolution-revealed-in-beauveria-bassiana-and-beauveria-brongniartii-genomes/
Gavin Prescott. “Host-range evolution revealed in Beauveria bassiana and Beauveria brongniartii genomes.” Scienmag, 11 September 2026, https://scienmag.com/host-range-evolution-revealed-in-beauveria-bassiana-and-beauveria-brongniartii-genomes/. Accessed 11 September 2026.
Gavin Prescott. “Host-range evolution revealed in Beauveria bassiana and Beauveria brongniartii genomes.” Scienmag. September 11, 2026. https://scienmag.com/host-range-evolution-revealed-in-beauveria-bassiana-and-beauveria-brongniartii-genomes/
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Tags: Beauveria bassiana genomeBeauveria brongniartii host-range evolutionBeauveria genome comparisonbiocontrol fungi genetic analysisbiopesticide development from Beauveria speciesbiopesticide fungal speciesbroad-spectrum versus specialist fungicommercial applications of biocontrol fungicomparative genomic analysis of entomopathogenic fungiecological strategies of generalist vs specialist fungientomopathogenic fungifungal adaptation to insect hostsfungal endophytes in plant protectiongene family divergence in pathogenic fungihost infection mechanisms in Beauveriahost specificity in Beauveriahost-range evolution in fungiinsect pathogen genomicsinsect-fungal interactionsmolecular basis of fungal pathogenicityplant-associated Beauveria speciessoilborne entomopathogenssoilborne parasite genomics
