Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in <i>Entomophthora muscae</i> and allied entomophthoralean fungi.

Abstract

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable <i>Entomophthora muscae</i> isolate that infects fruit flies. Our <i>E. muscae</i> assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that <i>E. muscae</i> and its closest allies possess genes that are likely homologs to the blue-light sensor <i>white-collar 1</i>, a <i>Neurospora crassa</i> gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that <i>E. muscae</i> diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with <i>E. muscae</i>'s species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the <i>E. muscae</i> species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.