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

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

Research output: Contribution to journalArticlepeer-review


Background: 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. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results: This 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. Conclusions: 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. 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.

Original languageEnglish (US)
Article number41
JournalBMC biology
Issue number1
StatePublished - Dec 2021


  • Chemoreceptor genes
  • Gene regulation
  • Insect adaptation
  • Insect immunity
  • Insect orthology
  • Metabolic detoxification genes
  • Muscid genomics
  • Opsin gene duplication
  • Stable fly genome

ASJC Scopus subject areas

  • Biotechnology
  • Structural Biology
  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences
  • Plant Science
  • Developmental Biology
  • Cell Biology


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