Confirmation and identification of parasitic stages of obligate endobionts (Harpellales) in blackflies (Simuliidae) by means of rRNA sequence data

De Novo Long-Read Genome Assembly and Annotation of the Mosquito Gut-Dwelling Fungus, Smittium minutisporum

Mosquito guts host a variety of microbes, yet fungi are often overlooked. Smittium (Harpellales, Zoopagomycota) comprises numerous species that are obligate symbionts residing in the hindgut of mosquito larvae. Despite their association with pathogen-bearing vectors, these fungal symbionts remain understudied, largely due to the lack of high-quality genome resources. This limitation has impeded a deeper understanding of their genome biology and adaptive strategies in relation to their mosquito hosts, which may hold significant epidemiological implications. To address this gap, we generated the first reference-quality genome assembly for this group of fungi, using PacBio HiFi long-reads for an axenic culture of Smittium minutisporum, originally isolated from the eastern treehole mosquito, Aedes triseriatus. The genome assembly consists of 53 contigs, spanning a total length of 32.5 Mb, and is predicted to encode 8,254 protein-coding genes, with repetitive regions constituting 25.22% of the genome. Notably, despite being highly contiguous and gap free, the Benchmarking Universal Single-Copy Ortholog analysis suggests a completeness score of 71.8%, implying unusual genome features, possibly shaped by adaptation and specialization within the mosquito gut. This high-quality genome resource will be invaluable for advancing our understanding of mosquito gut-dwelling fungi, their natural history, and their cryptic symbiosis with insect hosts.

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis

Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects.

Insect guts harbor various microbes that are important for host digestion, immune response, and disease dispersal in certain cases. Bacteria, which are among the primary endosymbionts, have been studied extensively. However, fungi, which are also frequently encountered, are poorly known with respect to their biology within the insect guts. To understand the genomic features and related biology, we produced the whole-genome sequences of nine gut commensal fungi from disease-bearing insects (black flies, midges, and mosquitoes). The results show that insect gut fungi tend to have low GC content across their genomes. By comparing these commensals with entomopathogenic and free-living fungi that have available genome sequences, we found a universal core gene toolbox that is unique and thus potentially important for the insect-fungus symbiosis. This comparative work also uncovered different host invasion strategies employed by insect pathogens and commensals, as well as a model system to study ancient fungal genome duplication within the gut of insects.

Examining new phylogenetic markers to uncover the evolutionary history of early-diverging fungi: comparing MCM7, TSR1 and rRNA genes for single- and multi-gene analyses of the Kickxellomycotina

The recently recognised protein-coding genes MCM7 and TSR1 have shown significant promise for phylogenetic resolution within the Ascomycota and Basidiomycota, but have remained unexamined within other fungal groups (except for Mucorales). We designed and tested primers to amplify these genes across early-diverging fungal clades, with emphasis on the Kickxellomycotina, zygomycetous fungi with characteristic flared septal walls forming pores with lenticular plugs. Phylogenetic tree resolution and congruence with MCM7 and TSR1 were compared against those inferred with nuclear small (SSU) and large subunit (LSU) rRNA genes. We also combined MCM7 and TSR1 data with the rDNA data to create 3- and 4-gene trees of the Kickxellomycotina that help to resolve evolutionary relationships among and within the core clades of this subphylum. Phylogenetic inference suggests that Barbatospora, Orphella, Ramicandelaber and Spiromyces may represent unique lineages. It is suggested that these markers may be more broadly useful for phylogenetic studies among other groups of early-diverging fungi.

Dipteran-associated Harpellales from lowland and submontane tropical rain forests of Veracruz (Mexico)

We report on the species of Harpellales found in dipteran hosts during two surveys (32 field d) in the state of Veracruz, Mexico. One new morphospecies, Genistellospora dorsicaudata, is described with particular attention to the position of the terminal cell associated with fully developed fertile thalli bearing sexual spores. We emend the description of G. guanacastensis to include morphometrics on the zygospores, based on discovery of the sexual spores for that species in our collections. Thirteen other previously described species, which are new for Mexico, include G. homothallica, Pennella montana, Simuliomyces microsporus, Smittium aciculare, S. brasiliense (in a new host type), S. culisetae, S. dipterorum, S. microsporum, S. simulii and the unbranched species Harpella melusinae, H. tica, Stachylina grandispora and S. paucispora. Some species have been described but not named, specifically one each of Harpella, Pennella and Smittium. All taxa are identified morphologically, illustrated and additional details on their ecology are provided.

Morphological differences of symbiotic fungi Smittium culisetae (Harpellales: Legeriomycetaceae) in different Dipteran hosts

Harpellales (Legeriomycetaceae, Zygomycota) or 'trichomycetes' are fungi that inhabit the digestive tracts of arthropods such as insects, millipedes, and crustaceans. In the current study we examined changes in 5 morphological characters of Smittium culisetae (Harpellales: Legeriomycetaceae) between the two dipteran (mosquito, black fly) hosts reared under 3 different temperatures (17, 22, 30 degrees C). Both host and temperature had a pervasive effect on the linear dimension of trichospores, their generative cells and hyphae width. At 30 degrees C the mean size of all 5 morphological characters were consistently larger in fungus taken from the mosquito host than from the black fly host. At 17 degrees C and 22 degrees C, however, there were no consistent patterns. The effect of host was so pronounced that it could be accurately determined which host S. culisetae colonised based on differences in linear morphology. Such changes in fungal morphology between hosts have important ramifications for the morphologically based taxonomy of this group.