The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Pia U Olafson,José M C Ribeiro,Christopher J Holmes,David B Taylor,Sonja L Swiger,Serap Aksoy,Panagiotis Ioannidis,Emily C Jennings,Wesley C Warren,Terence Murphy ,Sing Hoi Sze ,Gareth L Maslen ,Megan Davis,Richard P Meisel ,Matthew T Weirauch,Greta Buckmeier,Hugh M Robertson,David R Nelson,Scott J Emrich,Tyler J Raszick,Daniel Lawson,John H Werren,Aaron M Tarone,Markus Friedrich,Evgeny M Zdobnov,Kennan Oyen ,Marc E Rothenberg ,Richard K Wilson,Perot Saelao,Justin Dykema,Evan N Jansen,Ellen O Martinson,Andrew J Rosendale,Geoffrey M Attardo,Timothy B Sackton,Dana Nayduch,Robert M Waterhouse,Craig J Coates,Joshua B Benoit

doi:10.1186/s12915-021-00975-9

Abstract

BackgroundThe stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Highlights

The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone
The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest
This study advances the knowledge of stable fly genomics and genetics to the breadth of other non-model, but extremely important, dipterans such as tsetse and house flies

Summary

Introduction

The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Flies from the Muscidae family commonly occupy these settings, including the nonbiting house fly and face fly and the blood-feeding (hematophagous) stable fly and horn fly. The stable fly’s painful bites disrupt livestock feeding behavior [3,4,5,6]; these bites can be numerous during heavy infestation, leading to reductions of productivity by over $2 billion USD [7]

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Conclusion