The genome sequence of the avian vampire fly (Philornis downsi), an invasive nest parasite of Darwin's finches in Galápagos

Abstract

The invasive avian vampire fly (Philornis downsi, Diptera: Muscidae) is considered one of the greatest threats to the endemic avifauna of the Galápagos Islands. The fly larvae parasitize nearly every passerine species, including Darwin's finches. Most P. downsi research to date has focused on the effects of the fly on avian host fitness and mitigation methods. A lag in research related to the genetics of this invasion demonstrates, in part, the need to develop full-scale genomic resources with which to address further questions within this system. In this study, an adult female P. downsi was sequenced to generate a high-quality genome assembly. We examined various features of the genome (e.g., coding regions and noncoding transposable elements) and carried out comparative genomics analysis against other dipteran genomes. We identified lists of gene families that are significantly expanding or contracting in P. downsi that are related to insecticide resistance, detoxification, and counter defense against host immune responses. The P. downsi genome assembly provides an important resource for studying the molecular basis of successful invasion in the Galápagos and the dynamics of its population across multiple islands. The findings of significantly changing gene families associated with insecticide resistance and immune responses highlight the need for further investigations into the role of different gene families in aiding the fly's successful invasion. Furthermore, this genomic resource provides a necessary tool to better inform future research studies and mitigation strategies aimed at minimizing the fly's impact on Galápagos birds.

Keywords: Darwin’s finches; Galápagos; avian vampire fly genome; insecticide resistance; parasitic invasion.

Figure 1

The avian vampire fly, P. downsi (A), parasitizes many endemic bird species of the Galápagos Islands, including the medium ground finch, Geospiza fortis (B). The fly is parasitic in its larval forms (C, bottom three) residing primarily in the nesting material. The larvae feed by chewing through the skin and feeding on the secreted blood and other fluids of avian hosts. Larvae then pupate (C, second from top) in the nest material and enclose (C, top) as adult flies. Photos courtesy of Sam Rowley (A), Kelly Ballantyne (B), and Sabrina McNew (C).

Figure 2

Landscape of transposable elements in P. downsi. (A) Comparison of repeat content and genome size across Diptera and its outgroup. (B) Repeat statistics on various classes of transposable elements across dipteran genomes.

Figure 3

Orthogroups in P. downsi. (A) Phylogenetic relationship between P. downsi and other seven dipteran species, estimated using alignments from 3069 orthogroups had singly copy orthogroups in each species. Horizontal bars for each species show number of orthogroups that are single-copy orthologs in all species, present in all species, present in most species, present in few species, and unique to the species. (B) Number of shared orthologs among all species. Each vertical line connecting dots indicates the number of gene families (in the y-axis) that are shared among species analyzed. Certain shared gene families among species or unique gene families within a species had low count (<19), hence not included in the figure.

Figure 4

Gene family evolution. (A) Number of genes in Cytochrome P450 gene family across Diptera. (B) Number of genes in various subfamilies of Cytochromes P450 gene family in G. morsitans, P. downsi, M. domestica, and D. melanogaster. (C) Number of genes in glutathione S-transferase gene family across Diptera. (D) Number of genes in various subfamilies of glutathione S-transferase gene family in G. morsitans, P. downsi, M. domestica, and D. melanogaster.