Genome Expansion and Specialized Adaptations of the Insect Pathogen Entomophthora muscae and Related Entomophthoralean Fungi

Core Concepts

Entomophthoralean fungi have extremely large genomes due to extensive proliferation of transposable elements, despite the presence of machinery to defend against them. Entomophthora muscae and its closest allies exhibit unique adaptations, including expanded families of peptidases, carbohydrate-active enzymes, and light-sensing proteins, that likely facilitate their specialized, biotrophic lifestyles as insect pathogens.

Abstract

This study presents a new, largely complete genome assembly for the insect pathogen Entomophthora muscae and uses a comparative genomics approach to provide insights into the biology of Entomophthorales, an understudied order of fungal insect pathogens.
The key findings are:

Entomophthoralean genomes are vastly expanded, reaching over 1 Gb in size, due to extensive proliferation of Ty3/Gypsy retrotransposons, despite the presence of machinery to defend against transposable elements.

E. muscae and its closest allies exhibit unique adaptations, including:

Expanded families of M16A peptidases and acid trehalases, likely facilitating utilization of insect host resources.
Enrichment of genes involved in light sensing and circadian rhythms, potentially enabling manipulation of host behavior.
A distinct suite of secreted catabolic enzymes, consistent with E. muscae's specialized, biotrophic lifestyle.

Phylogenetic relationships based on morphological characteristics do not always align with those inferred from molecular data, suggesting the need for taxonomic revision within the E. muscae species complex.

E. muscae has a high proportion of species-specific genes, many of which are predicted to be secreted, highlighting its unique adaptations compared to other entomophthoralean fungi.

Overall, this work provides a genomic foundation for understanding the unique biology of these understudied insect pathogens and identifies avenues for further exploration.

Stats

Entomophthora muscae genome size is 1.03 Gb.
Entomophthora muscae genome contains 39,703 predicted genes.
Entomophthora muscae genome has 81.3% complete fungal BUSCOs.
Entomophthora muscae genome contains 90.9% repetitive sequences, primarily Ty3/Gypsy retrotransposons.
Entomophthora muscae has 62 proteins containing M16A metallopeptidase domains, compared to 5, 3, and 2 in related fungi.
Entomophthora muscae has 99 genes containing rhodopsin family light-sensing domains, far more than related fungi.

Quotes

"Entomophthoralean genomes are very large compared to the vast majority of other fungal genomes, each exceeding 500 Mb."
"The impressive sizes of E. muscae and other entomophthoralean genomes do not appear to be a consequence of increased gene number."
"The majority of repeat content across these four family Entomophthoraceae genomes consists of Class I retrotransposons, specifically Ty3 (formerly called Gypsy) long terminal repeat (LTR) retrotransposons."
"E. muscae, E. maimaiga and Z. radicans show an increase in TcMar elements more recently than either of the Ty3 and LINE expansions."

Key Insights Distilled From

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

by Stajich,J. E... at www.biorxiv.org 09-16-2023

https://www.biorxiv.org/content/10.1101/2023.09.13.557621v2

Deeper Inquiries

How do the expanded transposable element and light-sensing gene families in Entomophthora muscae contribute to its specialized, biotrophic lifestyle and ability to manipulate insect host behavior?

In Entomophthora muscae, the expanded transposable element families, particularly the Ty3 retrotransposons, play a crucial role in genome expansion. These elements have likely contributed to the large genome size observed in E. muscae and other entomophthoralean fungi. The presence of these transposable elements can lead to genetic diversity, potentially facilitating adaptation to different host environments and enhancing the ability to manipulate insect host behavior. The proliferation of transposable elements may also contribute to the evolution of novel genes and functions, which could be involved in the specialized, biotrophic lifestyle of E. muscae.
Additionally, the presence of light-sensing gene families in E. muscae, such as homologs to the white-collar 1 gene, indicates the ability of the fungus to detect and respond to environmental light cues. This light-sensing capability is likely essential for regulating circadian rhythms and coordinating activities related to host manipulation. The ability to sense light may also play a role in the timing of spore release and other life cycle events, enhancing the fungus's efficiency in infecting and manipulating insect hosts.
Overall, the expanded transposable element and light-sensing gene families in E. muscae contribute to its specialized, biotrophic lifestyle by providing genetic diversity, facilitating adaptation to host environments, regulating circadian rhythms, and enhancing the ability to manipulate insect host behavior.

How do the evolutionary pressures and mechanisms that have led to the massive genome expansions observed across the Entomophthorales order, despite the presence of RNAi machinery to defend against transposable elements?

The massive genome expansions observed across the Entomophthorales order are likely the result of complex evolutionary pressures and mechanisms. Despite the presence of RNA interference (RNAi) machinery, which serves as a defense mechanism against transposable elements, these fungi have experienced extensive genome inflation. Several factors may contribute to this phenomenon:

Evolutionary Arms Race: The presence of transposable elements in the genome can lead to an evolutionary arms race between the host genome and the transposable elements. The continuous activity of transposable elements and their ability to evade host defenses may drive genome expansion as a mechanism for survival and adaptation.

Genetic Diversity and Adaptation: The proliferation of transposable elements can generate genetic diversity within the genome, providing raw material for adaptation to new environments and hosts. This genetic diversity may confer a selective advantage, leading to the retention of expanded genomes.

Functional Innovation: The expansion of genomes may also be driven by the acquisition of new genes and functions through transposable element activity. These new genes could contribute to the specialized biotrophic lifestyle of Entomophthorales fungi, allowing them to manipulate insect hosts and thrive in their unique ecological niches.

Regulation of Transposable Elements: While RNAi machinery can defend against transposable elements, the balance between transposable element activity and host defense mechanisms may vary across species. In some cases, the regulatory mechanisms may not be sufficient to prevent genome expansion, leading to the observed massive genomes in Entomophthorales.

In summary, the massive genome expansions in Entomophthorales despite the presence of RNAi machinery may be driven by evolutionary pressures such as the arms race with transposable elements, the need for genetic diversity and adaptation, functional innovation, and the intricate regulation of transposable elements within the genome.

Given the discrepancies between morphology-based and molecular-based phylogenies, what are the key morphological features that should be used to accurately delineate species boundaries within the Entomophthora muscae species complex?

To accurately delineate species boundaries within the Entomophthora muscae species complex, it is essential to consider a combination of morphological features that are consistent and reliable across different strains and populations. Key morphological features that can be used to differentiate species within the E. muscae complex include:

Conidiophore Structure: The morphology of conidiophores, including size, shape, branching patterns, and conidia production, can be a distinguishing characteristic among different species within the complex.

Host Specificity: The range of insect hosts infected by a particular strain can be a crucial factor in species delineation. Species within the E. muscae complex may exhibit varying host specificities, which can help differentiate them.

Behavioral Manipulation: The specific behavioral changes induced in infected insect hosts, such as summit disease or wing extension prior to death, can be unique to certain species and serve as diagnostic features.

Spore Characteristics: Differences in spore morphology, size, color, and other features can be used to differentiate species within the complex.

Physiological Traits: Physiological characteristics related to growth conditions, nutrient utilization, and metabolic pathways can also provide valuable information for species delineation.

Genetic Markers: Molecular techniques, such as DNA sequencing of specific genetic markers, can complement morphological analyses and provide additional resolution in species identification.

By integrating these morphological features and considering both traditional and molecular methods, researchers can more accurately delineate species boundaries within the Entomophthora muscae complex. This comprehensive approach can help overcome discrepancies between morphology-based and molecular-based phylogenies and enhance our understanding of the diversity and evolution of these fascinating insect-pathogenic fungi.