Comparative transcriptomics reveal host‐specific nucleotide variation in entomophthoralean fungi

Abstract

Obligate parasites are under strong selection to increase exploitation of their host to survive while evading detection by host immune defences. This has often led to elaborate pathogen adaptations and extreme host specificity. Specialization on one host, however, often incurs a trade-off influencing the capacity to infect alternate hosts. Here, we investigate host adaptation in two morphologically indistinguishable and closely related obligate specialist insect-pathogenic fungi from the phylum Entomophthoromycota, Entomophthora muscae sensu stricto and E. muscae sensu lato, pathogens of houseflies (Musca domestica) and cabbage flies (Delia radicum), respectively. We compared single nucleotide polymorphisms within and between these two E. muscae species using 12 RNA-seq transcriptomes from five biological samples. All five isolates contained intra-isolate polymorphisms that segregate in 50:50 ratios, indicative of genetic duplication events or functional diploidy. Comparative analysis of dN/dS ratios between the multinucleate E. muscae s.str. and E. muscae s.l. revealed molecular signatures of positive selection in transcripts related to utilization of host lipids and the potential secretion of toxins that interfere with the host immune response. Phylogenetic comparison with the nonobligate generalist insect-pathogenic fungus Conidiobolus coronatus revealed a gene-family expansion of trehalase enzymes in E. muscae. The main sugar in insect haemolymph is trehalose, and efficient sugar utilization was probably important for the evolutionary transition to obligate insect pathogenicity in E. muscae. These results support the hypothesis that genetically based host specialization in specialist pathogens evolves in response to the challenge of using resources and dealing with the immune system of different hosts.

Logistic growth of the host‐specific obligate insect pathogenic fungus Entomophthora muscae in house flies (Musca domestica)

“…no. ) obtained from a genomewide transcriptome data set of E. muscae (De Fine Licht et al., ). BLASTn searches against the house fly genome (Scott et al.…”

“…no. KU756097) obtained from a genomewide transcriptome data set of E. muscae (De Fine Licht et al, 2017). BLASTn searches against the house fly genome (Scott et al 2014) and uninfected control samples were used to ensure that primers did not crossamplify host DNA.…”

Robust manipulation of the behavior ofDrosophila melanogasterby a fungal pathogen in the laboratory

“…However, it is generally thought that E. muscae evades the host immune response once inside the fly because it grows without a cell wall (i.e. protoplastically) and therefore does not present antigens that can alert the fly immune system to infection [48,49]. Examining expression patterns of all genes annotated as having immune function, we see a large induction of immune gene expression at 24-48 hours which includes genes both involved in the melanization response and genes that specifically respond to fungal infection.…”

A genome scan of diversifying selection in Ophiocordyceps zombie‐ant fungi suggests a role for enterotoxins in co‐evolution and host specificity

“…Trehalases, in particular, probably play an important role in this respect. Indeed, the fly pathogen Entomophthora muscae (Entomophthorales) carries more trehalase‐encoding genes in its genome than its close relative, the generalist Conidiobolus coronatus, which is a nonobligate pathogen (De Fine Licht, Jensen, & Eilenberg, ). We identified two trehalases with no positive selection signature as conserved across all species.…”