Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

Abstract

Background: Blow flies (Diptera: Calliphoridae) are important medical, veterinary and forensic insects encompassing 8 % of the species diversity observed in the calyptrate insects. Few genomic resources exist to understand the diversity and evolution of this group.

Results: We present the hybrid (short and long reads) draft assemblies of the male and female genomes of the common North American blow fly, Phormia regina (Diptera: Calliphoridae). The 550 and 534 Mb draft assemblies contained 8312 and 9490 predicted genes in the female and male genomes, respectively; including > 93 % conserved eukaryotic genes. Putative X and Y chromosomes (21 and 14 Mb, respectively) were assembled and annotated. The P. regina genomes appear to contain few mobile genetic elements, an almost complete absence of SINEs, and most of the repetitive landscape consists of simple repetitive sequences. Candidate gene approaches were undertaken to annotate insecticide resistance, sex-determining, chemoreceptors, and antimicrobial peptides.

Conclusions: This work yielded a robust, reliable reference calliphorid genome from a species located in the middle of a calliphorid phylogeny. By adding an additional blow fly genome, the ability to tease apart what might be true of general calliphorids vs. what is specific of two distinct lineages now exists. This resource will provide a strong foundation for future studies into the evolution, population structure, behavior, and physiology of all blow flies.

Keywords: Blow fly; Calliphoridae; Genome; Phormia regina; Sex determination; X chromosome; Y chromosome.

Fig. 1

GO term classification of the 3 functional categories (biological processes, molecular function and cellular component) of the predicted genes in the male and female genome assemblies

Fig. 2

The top 35 KEGG biological pathways of the male and female gene sets extracted from the Blast2GO analysis

Fig. 3

Predicted gene structure of the sex determining gene daughterless for the female (F) and male (M) P. regina. The red boxes represent the exon, the grey boxes inclusive of the red represent the mRNA, and the black line represent the intron. Image is not drawn to scale

Fig. 4

Transposable element accumulation in the female (a) and male (b) Phormia regina genome assemblies. Kimura 2-parameter distances were calculated between transposable element insertions in the genome and the homologous element in the dipteran Repbase library. Larger divergences indicate elements with larger mutation loads, and by extension, were deposited in the genome in the more distant past. Less than 40 SINE elements are present in either the female or male assemblies and are not shown here. Transposable elements are slightly more abundant in the female genome assembly. The accumulation of female specific repeats (c) follows that of the whole genome in general