Genomic signatures and insights into host niche adaptation of the entomopathogenic fungus Metarhizium humberi

Abstract

The genus Metarhizium is composed of species used in biological control programs of agricultural pests worldwide. This genus includes common fungal pathogen of many insects and mites and endophytes that can increase plant growth. Metarhizium humberi was recently described as a new species. This species is highly virulent against some insect pests and promotes growth in sugarcane, strawberry, and soybean crops. In this study, we sequenced the genome of M. humberi, isolate ESALQ1638, and performed a functional analysis to determine its genomic signatures and highlight the genes and biological processes associated with its lifestyle. The genome annotation predicted 10633 genes in M. humberi, of which 92.0% are assigned putative functions, and ∼17% of the genome was annotated as repetitive sequences. We found that 18.5% of the M. humberi genome is similar to experimentally validated proteins associated with pathogen-host interaction. Compared to the genomes of eight Metarhizium species, the M. humberi ESALQ1638 genome revealed some unique traits that stood out, e.g., more genes functionally annotated as polyketide synthases (PKSs), overrepresended GO-terms associated to transport of ions, organic and amino acid, a higher percentage of repetitive elements, and higher levels of RIP-induced point mutations. The M. humberi genome will serve as a resource for promoting studies on genome structure and evolution that can contribute to research on biological control and plant biostimulation. Thus, the genomic data supported the broad host range of this species within the generalist PARB clade and suggested that M. humberi ESALQ1638 might be particularly good at producing secondary metabolites and might be more efficient in transporting amino acids and organic compounds.

Keywords: entomopathogenic fungus; genomic features; host adaptation; specialization.

Figure 1

Dot-plots representing whole-genome comparison between M. humberi ESALQ1638 and 10 other Metarhizium strains. The comparison was performed using NUCmer 3.1 for each pair of genomes. Scaffolds of M. humberi ESALQ1638 are displayed by decreasing size along the x-axis, matching scaffolds of the compared genome are shown on the y-axis. Homologous regions are plotted as diagonal lines with dots at the starting and endpoints. Color coding indicates an aligned strand, with blue representing the main strand and red showing the reverse strand.

Figure 2

Maximum likelihood tree using concatenated protein sequences of 3131 orthologous genes with exactly one ortholog in the genomes of A. niger SH23; B. bassiana ARSEEF28603; F. verticillioides 7600; M. acridum CQMa1023; M. album ARSEF1941; M. anisopliae ARSEF5493, BRIP53293 and ESALQE6; M. brunneum ARSEF32973; M. guizhouense ARSEF9773; M. humberi ESALQ1638; M. majus ARSEF2973; M. rileyi RCEF48713; M. robertsii ARSEF233; and T. harzianum T67763. The evolutionary history was inferred by using the maximum likelihood method with an LG model. The tree is drawn to scale, with branch lengths measured in the number of substitutions per position.

Figure 3

Venn diagram comparing the orthologous of M. humberi ESALQ1638 shared between M. rileyi RCEF48713, M. robertsii ARSEF23, M. anisopliae BRIP53293, and M. brunneum ARSEF3297 and enzymes annotated to shared orthologous (EC: enzyme code).

Figure 4

Interpro categories and number of predicted protein-coding genes from each category found in the genome of M. humberi ESALQ1638, eight Metarhizium species, B. bassiana ARSEF2860, A. niger SH-2, F. verticillioides 7600, and T. harzianum T6776. Mrob (M. robertsii ARSEF23); ManiA (M. anisopliae ARSEF549); ManiB (M. anisopliae BRIP53293); ManiE (M. anisopliae ESALQE6); Mbru (M. brunneum ARSEF3297); Mgui (M. guizhouense ARSEF977); Mmaj (M. majus ARSEF297); Macr (M. acridum CQMa102); Malb (M. album ARSEF1941); and Mril (M. rileyi RCEF4871).

Figure 5

Interpro categories and number of predicted protein-coding genes from each category found in the genome of M. humberi ESALQ1638, eight Metarhizium species, B. bassiana ARSEF2860, A. niger SH-2, F. verticillioides 7600, and T. harzianum T6776. Mrob (M. robertsii ARSEF23); ManiA (M. anisopliae ARSEF549); ManiB (M. anisopliae BRIP53293); ManiE (M. anisopliae ESALQE6); Mbru (M. brunneum ARSEF3297); Mgui (M. guizhouense ARSEF977); Mmaj (M. majus ARSEF297); Macr (M. acridum CQMa102); Malb (M. album ARSEF1941); and Mril (M. rileyi RCEF4871).

Figure 6

Selected enriched Gene Ontology terms (Biological Process) in rapidly evolving gene families of 11 Metarhizium genomes belonging to eight species. Shown are all significantly overrepresented Biological Process GO terms that contained the terms “biosynthetic process” (BP, top), “metabolic process” (MP, middle), and “transport”/“import”/“export” (T, bottom). The P-value for each GO term and genome is indicated by color; the cutoff for significance was 0.05. A plot containing all overrepresented GO terms from all three ontology categories can be found on the Gitlab repository associated with this publication: https://gitlab.nibio.no/simeon/iwanicki_et_al_21/-/tree/master/Cafe_Aug21.