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Ajayi OM, Oyen KJ, Davies B, Finch G, Piller BD, Harmeyer AA, Wendeln K, Perretta C, Rosendale AJ, Benoit JB. Egg hatching success is influenced by the time of thermal stress in four hard tick species. J Med Entomol 2024; 61:110-120. [PMID: 37889857 PMCID: PMC10784778 DOI: 10.1093/jme/tjad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Ticks are blood-feeding arthropods responsible for the transmission of disease-causing pathogens to a wide range of vertebrate hosts, including livestock and humans. Tick-borne diseases have been implicated in significant economic losses to livestock production, and this threat will increase as these obligate parasites widen their geographical ranges. Similar to other ectotherms, thermal stress due to changing global temperatures has been shown to influence tick survival and distribution. However, studies on the influence of extreme temperatures in ticks have focused on advanced, mobile stages, ignoring immobile stages that cannot move to more favorable microhabitats. In this study, low- and high-temperature regimens were assessed in relation to egg viability for hard tick species-Amblyomma maculatum (Gulf Coast tick), Ixodes scapularis (black-legged tick), Dermacentor variabilis (American dog tick), and Rhipicephalus sanguineus (Brown dog tick). Tick eggs exposed early in development (freshly laid during early embryo development) were significantly more susceptible to thermal stress when compared with those exposed later in development (late embryo development denoted by a fecal spot). Based on our studies, differences in egg hatching success among treatments were greater than in hatching success when comparing species. Lastly, there was evidence of extreme thermal exposure significantly altering the hatching times of tick eggs for specific treatments. These results provide insights into the critical period for tick egg viability in relation to thermal exposure and tick survival associated with stress and climate change.
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Affiliation(s)
- Oluwaseun M Ajayi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Kennan J Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
- Animal Diseases Research Unit, USDA-ARS, 3003 ADBF, Pullman, WA, USA
| | - Benjamin Davies
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Geoffrey Finch
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Benjamin D Piller
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Alison A Harmeyer
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Katherine Wendeln
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Carlie Perretta
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Andrew J Rosendale
- Biology Department, Mount St. Joseph University, Cincinnati, OH 45233, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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2
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Labbé F, Abdeladhim M, Abrudan J, Araki AS, Araujo RN, Arensburger P, Benoit JB, Brazil RP, Bruno RV, Bueno da Silva Rivas G, Carvalho de Abreu V, Charamis J, Coutinho-Abreu IV, da Costa-Latgé SG, Darby A, Dillon VM, Emrich SJ, Fernandez-Medina D, Figueiredo Gontijo N, Flanley CM, Gatherer D, Genta FA, Gesing S, Giraldo-Calderón GI, Gomes B, Aguiar ERGR, Hamilton JGC, Hamarsheh O, Hawksworth M, Hendershot JM, Hickner PV, Imler JL, Ioannidis P, Jennings EC, Kamhawi S, Karageorgiou C, Kennedy RC, Krueger A, Latorre-Estivalis JM, Ligoxygakis P, Meireles-Filho ACA, Minx P, Miranda JC, Montague MJ, Nowling RJ, Oliveira F, Ortigão-Farias J, Pavan MG, Horacio Pereira M, Nobrega Pitaluga A, Proveti Olmo R, Ramalho-Ortigao M, Ribeiro JMC, Rosendale AJ, Sant'Anna MRV, Scherer SE, Secundino NFC, Shoue DA, da Silva Moraes C, Gesto JSM, Souza NA, Syed Z, Tadros S, Teles-de-Freitas R, Telleria EL, Tomlinson C, Traub-Csekö YM, Marques JT, Tu Z, Unger MF, Valenzuela J, Ferreira FV, de Oliveira KPV, Vigoder FM, Vontas J, Wang L, Weedall GD, Zhioua E, Richards S, Warren WC, Waterhouse RM, Dillon RJ, McDowell MA. Genomic analysis of two phlebotomine sand fly vectors of leishmania from the new and old World. PLoS Negl Trop Dis 2023; 17:e0010862. [PMID: 37043542 PMCID: PMC10138862 DOI: 10.1371/journal.pntd.0010862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 04/27/2023] [Accepted: 02/13/2023] [Indexed: 04/13/2023] Open
Abstract
Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.
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Affiliation(s)
- Frédéric Labbé
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Maha Abdeladhim
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jenica Abrudan
- Genomic Sciences & Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alejandra Saori Araki
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ricardo N Araujo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona, California, United States of America
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | | | - Rafaela V Bruno
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gustavo Bueno da Silva Rivas
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Vinicius Carvalho de Abreu
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jason Charamis
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Greece
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
| | - Iliano V Coutinho-Abreu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, California, United States of America
| | | | - Alistair Darby
- Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom
| | - Viv M Dillon
- Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | | | - Nelder Figueiredo Gontijo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Catherine M Flanley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Fernando A Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sandra Gesing
- Discovery Partners Institute, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Gloria I Giraldo-Calderón
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
- Dept. Ciencias Biológicas & Dept. Ciencias Básicas Médicas, Universidad Icesi, Cali, Colombia
| | - Bruno Gomes
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - James G C Hamilton
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Omar Hamarsheh
- Department of Life Sciences, Faculty of Science and Technology, Al-Quds University, Jerusalem, Palestine
| | - Mallory Hawksworth
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Jacob M Hendershot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Paul V Hickner
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, Texas, United States of America
| | - Jean-Luc Imler
- CNRS-UPR9022 Institut de Biologie Moléculaire et Cellulaire and Faculté des Sciences de la Vie-Université de Strasbourg, Strasbourg, France
| | - Panagiotis Ioannidis
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Charikleia Karageorgiou
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Genomics Group - Bioinformatics and Evolutionary Biology Lab, Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
| | - Ryan C Kennedy
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Andreas Krueger
- Medical Entomology Branch, Dept. Microbiology, Bundeswehr Hospital, Hamburg, Germany
- Medical Zoology Branch, Dept. Microbiology, Central Bundeswehr Hospital, Koblenz, Germany
| | - José M Latorre-Estivalis
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Petros Ligoxygakis
- Laboratory of Cell Biology, Development and Genetics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Patrick Minx
- Donald Danforth Plant Science Center, Olivette, Missouri, United States of America
| | - Jose Carlos Miranda
- Laboratório de Imunoparasitologia, CPqGM, Fundação Oswaldo Cruz, Bahia, Brazil
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronald J Nowling
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - Fabiano Oliveira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | | | - Marcio G Pavan
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
- Laboratório de Transmissores de Hematozoários, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Marcos Horacio Pereira
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Andre Nobrega Pitaluga
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, Brazil
| | - Roenick Proveti Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcelo Ramalho-Ortigao
- F. Edward Hebert School of Medicine, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - José M C Ribeiro
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Andrew J Rosendale
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Mauricio R V Sant'Anna
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nágila F C Secundino
- Laboratory of Medical Entomology, René Rachou Institute-FIOCRUZ, Belo Horizonte, Brazil
| | - Douglas A Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | | | | | - Nataly Araujo Souza
- Laboratory Interdisciplinar em Vigilancia Entomologia em Diptera e Hemiptera, Fiocruz, Rio de Janeiro, Brazil
| | - Zainulabueddin Syed
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Samuel Tadros
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | | | - Erich L Telleria
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | | | - João Trindade Marques
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Zhijian Tu
- Fralin Life Science Institute and Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Maria F Unger
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jesus Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Flávia V Ferreira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Karla P V de Oliveira
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Felipe M Vigoder
- Universidade Federal do Rio de Janeiro, Instituto de Biologia. Rio de Janeiro, Brazil
| | - John Vontas
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Pesticide Science Lab, Department of Crop Science, Agricultural University of Athens, Athens Greece
| | - Lihui Wang
- Donald Danforth Plant Science Center, Olivette, Missouri, United States of America
| | - Gareth D Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine (LSTM), Liverpool, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Elyes Zhioua
- Vector Ecology Unit, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
| | - Robert M Waterhouse
- Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Rod J Dillon
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Mary Ann McDowell
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
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Pathak A, Chakraborty S, Oyen K, Rosendale AJ, Benoit JB. Dual assessment of transcriptional and metabolomic responses in the American dog tick following exposure to different pesticides and repellents. Ticks Tick Borne Dis 2022; 13:102033. [PMID: 36099731 PMCID: PMC9971363 DOI: 10.1016/j.ttbdis.2022.102033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 02/03/2023]
Abstract
The American dog tick, Dermacentor variabilis, is a major pest to humans and animals, serving as a vector to Rickettsia rickettsii, a bacterium responsible for Rocky Mountain spotted fever, and Francisella tularensis, which is responsible for tularemia. Although several tactics for management have been deployed, very little is known about the molecular response following pesticidal treatments in ticks. In this study, we used a combined approach utilizing transcriptomics and metabolomics to understand the response of the American dog tick to five common pesticides (amitraz, chlorpyrifos, fipronil, permethrin, and propoxur), and analyzed previous experimental data utilizing DEET repellent. Exposure to different chemicals led to significant differential expression of a varying number of transcripts, where 42 were downregulated and only one was upregulated across all treatments. A metabolomic analysis identified significant changes in acetate and aspartate levels following exposure to chlorpyrifos and propoxur, which was attributed to reduced cholinesterase activity. Integrating the metabolomics study with RNA-seq analysis, we found the physiological manifestations of the combined metabolic and transcriptional differences, revealing several novel biomolecular pathways. In particular, we discovered the downregulation of amino sugar metabolism and methylhistidine metabolism after permethrin exposure, as well as an upregulation of glutamate metabolism in amitraz treated samples. Understanding these altered biochemical pathways following pesticide and repellent exposure can help us formulate more effective chemical treatments to reduce the burden of ticks.
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Affiliation(s)
- Atit Pathak
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Souvik Chakraborty
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Kennan Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211; Biology Department, Mount St. Joseph University, Cincinnati, OH, 45233
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211.
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4
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Rosendale AJ, Leonard RK, Patterson IW, Arya T, Uhran MR, Benoit JB. Metabolomic and transcriptomic responses of ticks during recovery from cold shock reveal mechanisms of survival. J Exp Biol 2022; 225:275159. [PMID: 35179594 DOI: 10.1242/jeb.236497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/16/2022] [Indexed: 11/20/2022]
Abstract
Ticks are blood-feeding ectoparasites but spend most of their life off-host where they may have to tolerate low winter temperatures. Rapid cold-hardening (RCH) is a process commonly used by arthropods, including ticks, to improve survival of acute low temperature exposure. However, little is known about the underlying mechanisms in ticks associated with RCH, cold shock, and recovery from these stresses. In the present study, we investigated the extent to which RCH influences gene expression and metabolism during recovery from cold stress in Dermacentor variabilis, the American dog tick, using a combined transcriptomics and metabolomics approach. Following recovery from RCH, 1,860 genes were differentially expressed in ticks, whereas only 99 genes responded during recovery to direct cold shock. Recovery from RCH resulted in an upregulation of various pathways associated with ion binding, transport, metabolism, and cellular structures seen in the response of other arthropods to cold. The accumulation of various metabolites, including several amino acids and betaine, corresponded to transcriptional shifts in the pathways associated with these molecules, suggesting congruent metabolome and transcriptome changes. Ticks receiving exogenous betaine and valine demonstrated enhanced cold tolerance, suggesting cryoprotective effects of these metabolites. Overall, many of the responses during recovery from cold shock in ticks were similar to those observed in other arthropods, but several adjustments may be distinct from other currently examined taxa.
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Affiliation(s)
- Andrew J Rosendale
- Biology Department, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Ryan K Leonard
- Biology Department, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Isaac W Patterson
- Biology Department, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Thomas Arya
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Melissa R Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
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5
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Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze SH, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. BMC Biol 2021; 19:150. [PMID: 34325695 PMCID: PMC8320157 DOI: 10.1186/s12915-021-01098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Pia U Olafson
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California - Davis, Davis, CA, USA
| | - Greta Buckmeier
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Xiaoting Chen
- The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Craig J Coates
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - Megan Davis
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Justin Dykema
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Scott J Emrich
- Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Evan N Jansen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel Lawson
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Gareth L Maslen
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dana Nayduch
- Arthropod-borne Animal Diseases Research Unit, USDA-ARS, Manhattan, KS, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kennan J Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Tyler J Raszick
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - José M C Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Timothy B Sackton
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Perot Saelao
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Sonja L Swiger
- Department of Entomology, Texas A&M AgriLife Research and Extension Center, Stephenville, TX, USA
| | - Sing-Hoi Sze
- Department of Computer Science & Engineering, Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX, USA
| | - Aaron M Tarone
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - David B Taylor
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, USA
| | - Wesley C Warren
- University of Missouri, Bond Life Sciences Center, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,College of Medicine, Ohio State University, Columbus, OH, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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6
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Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MJM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BM, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol 2021; 12:1099-1188. [PMID: 32442304 PMCID: PMC7455281 DOI: 10.1093/gbe/evaa106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
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Affiliation(s)
- Jan Philip Oeyen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Lead Contact
| | | | | | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | | | - Anja Buttstedt
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Germany
| | - Federica Calevro
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Elizabeth I Cash
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University.,Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Hubert Charles
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Andrew G Cridge
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Biology, Georgia Southern University, Statesboro.,Department of Entomology, Purdue University, West Lafayette
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Ewald Große-Wilde
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CULS), Praha 6-Suchdol, Czech Republic
| | - Cameron Gudobba
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Frank Hauser
- Department of Biology, University of Copenhagen, Denmark
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emmanuelle Jacquin-Joly
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Versailles, France
| | | | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, Rochester
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Peter Lesný
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | - Mackenzie Lovegrove
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sebastian Martin
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | | | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Nicolas Montagné
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Victoria C Moris
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Monica Munoz-Torres
- Berkeley Bioinformatics Open-source Projects (BBOP), Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Shwetha Canchi Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, Kansas
| | - Nicolas Parisot
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Thomas Pauli
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Ralph S Peters
- Arthropoda Department, Center for Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Emma Persyn
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Institute for Insect Biotechnology, University of Gießen, Germany.,Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | | | - Felipe A Simao
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - John Skelly
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | | | - Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati.,Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida
| | - Megumi Sumitani
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Owashi, Tsukuba, Japan
| | - Elise M Szuter
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University
| | - Olivia Tidswell
- Biochemistry Department, University of Otago, Dunedin, New Zealand.,Zoology Department, University of Cambridge, United Kingdom
| | | | - Lucia Vedder
- Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Daisuke S Yamamoto
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Yakushiji, Shimotsuke, Japan
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tanja Ziesmann
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Masatsugu Hatakeyama
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
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7
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Davies B, Rosendale AJ, Gantz JD, Lee RE, Denlinger DL, Benoit JB. Cross-tolerance and transcriptional shifts underlying abiotic stress in the seabird tick, Ixodes uriae. Polar Biol 2021. [DOI: 10.1007/s00300-021-02887-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Fieler AM, Rosendale AJ, Farrow DW, Dunlevy MD, Davies B, Oyen K, Xiao Y, Benoit JB. Larval thermal characteristics of multiple ixodid ticks. Comp Biochem Physiol A Mol Integr Physiol 2021; 257:110939. [PMID: 33794367 PMCID: PMC8500258 DOI: 10.1016/j.cbpa.2021.110939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/26/2022]
Abstract
Temperature limits the geographic ranges of several tick species. Little is known about the thermal characteristics of these pests outside of a few studies on survival related to thermal tolerance. In this study, thermal tolerance limits, thermal preference, and the impact of temperature on activity levels and metabolic rate were examined in larvae for six species of ixodid ticks. Tolerance of low temperatures ranged from -15 to -24 °C with Dermacentor andersoni surviving the lowest temperatures. High temperature survival ranged from 41 to 47 °C, with Rhipicephalus sanguineus sensu lato having the highest upper lethal limit. Ixodes scapularis showed the lowest survival at both low and high temperatures. Thermal preference temperatures were tested from 0 to 41 °C. The majority of species preferred temperatures between 17 and 22 °C, while Dermacentor variabilis preferred significantly lower temperatures, near 12 °C. Overall activity was measured across a range of temperatures from 10 to 60 °C, and most tick species had the greatest activity near 30 °C. Metabolic rate was the greatest between 30 and 40 °C for all tick species and was relatively stable from 5 to 20 °C. The optimal temperature for tick larvae is likely near the thermal preference for each species, where oxygen consumption is low and activity occurs that will balance questing and conservation of nutrient reserves. In summary, tick species vary greatly in their thermal characteristics, and our results will be critical to predict distribution of these ectoparasites with changing climates.
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Affiliation(s)
- Alicia M Fieler
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA; Department of Biology, Mount St. Joseph University, Cincinnati, OH, USA
| | - David W Farrow
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Megan D Dunlevy
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Benjamin Davies
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Kennan Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Yanyu Xiao
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
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9
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Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze SH, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. BMC Biol 2021; 19:41. [PMID: 33750380 PMCID: PMC7944917 DOI: 10.1186/s12915-021-00975-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/03/2021] [Indexed: 01/01/2023] Open
Abstract
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00975-9.
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Affiliation(s)
- Pia U Olafson
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California - Davis, Davis, CA, USA
| | - Greta Buckmeier
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Xiaoting Chen
- The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Craig J Coates
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - Megan Davis
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Justin Dykema
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Scott J Emrich
- Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Evan N Jansen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel Lawson
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Gareth L Maslen
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dana Nayduch
- Arthropod-borne Animal Diseases Research Unit, USDA-ARS, Manhattan, KS, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kennan J Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Tyler J Raszick
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - José M C Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Timothy B Sackton
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Perot Saelao
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Sonja L Swiger
- Department of Entomology, Texas A&M AgriLife Research and Extension Center, Stephenville, TX, USA
| | - Sing-Hoi Sze
- Department of Computer Science & Engineering, Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX, USA
| | - Aaron M Tarone
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - David B Taylor
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, USA
| | - Wesley C Warren
- University of Missouri, Bond Life Sciences Center, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,College of Medicine, Ohio State University, Columbus, OH, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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10
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Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Vargas Jentzsch IM, Oliver JE, Poelchau MF, Rajarapu SP, Schneweis DJ, Snoeck S, Taning CNT, Wei D, Widana Gamage SMK, Hughes DST, Murali SC, Bailey ST, Bejerman NE, Holmes CJ, Jennings EC, Rosendale AJ, Rosselot A, Hervey K, Schneweis BA, Cheng S, Childers C, Simão FA, Dietzgen RG, Chao H, Dinh H, Doddapaneni HV, Dugan S, Han Y, Lee SL, Muzny DM, Qu J, Worley KC, Benoit JB, Friedrich M, Jones JW, Panfilio KA, Park Y, Robertson HM, Smagghe G, Ullman DE, van der Zee M, Van Leeuwen T, Veenstra JA, Waterhouse RM, Weirauch MT, Werren JH, Whitfield AE, Zdobnov EM, Gibbs RA, Richards S. Correction to: Genome-enabled insights into the biology of thrips as crop pests. BMC Biol 2020; 18:169. [PMID: 33198778 PMCID: PMC7670811 DOI: 10.1186/s12915-020-00915-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Aaron A Baumann
- Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA
| | - Sulley Ben-Mahmoud
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Panagiotis Ioannidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Vassilika Vouton, 70013, Heraklion, Greece.,Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Jonathan E Oliver
- Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA
| | | | - Swapna Priya Rajarapu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Derek J Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Simon Snoeck
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Department of Biology, University of Washington, Seattle, WA, 98105, USA
| | - Clauvis N T Taning
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dong Wei
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | | | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | | | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.,Department of Biology, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Andrew Rosselot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Kaylee Hervey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brandi A Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | | | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, QLD, St. Lucia, 4072, Australia
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.,School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | - Diane E Ullman
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | | | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Jan A Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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11
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Finch G, Nandyal S, Perretta C, Davies B, Rosendale AJ, Holmes CJ, Gantz JD, Spacht DE, Bailey ST, Chen X, Oyen K, Didion EM, Chakraborty S, Lee RE, Denlinger DL, Matter SF, Attardo GM, Weirauch MT, Benoit JB. Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability. Sci Rep 2020; 10:19791. [PMID: 33188214 PMCID: PMC7666147 DOI: 10.1038/s41598-020-76139-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 10/07/2020] [Indexed: 12/13/2022] Open
Abstract
The Antarctic midge, Belgica antarctica, is a wingless, non-biting midge endemic to Antarctica. Larval development requires at least 2 years, but adults live only 2 weeks. The nonfeeding adults mate in swarms and females die shortly after oviposition. Eggs are suspended in a gel of unknown composition that is expressed from the female accessory gland. This project characterizes molecular mechanisms underlying reproduction in this midge by examining differential gene expression in whole males, females, and larvae, as well as in male and female accessory glands. Functional studies were used to assess the role of the gel encasing the eggs, as well as the impact of stress on reproductive biology. RNA-seq analyses revealed sex- and development-specific gene sets along with those associated with the accessory glands. Proteomic analyses were used to define the composition of the egg-containing gel, which is generated during multiple developmental stages and derived from both the accessory gland and other female organs. Functional studies indicate the gel provides a larval food source as well as a buffer for thermal and dehydration stress. All of these function are critical to juvenile survival. Larval dehydration stress directly reduces production of storage proteins and key accessory gland components, a feature that impacts adult reproductive success. Modeling reveals that bouts of dehydration may have a significant impact on population growth. This work lays a foundation for further examination of reproduction in midges and provides new information related to general reproduction in dipterans. A key aspect of this work is that reproduction and stress dynamics, currently understudied in polar organisms, are likely to prove critical in determining how climate change will alter their survivability.
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Affiliation(s)
- Geoffrey Finch
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Sonya Nandyal
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Carlie Perretta
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Benjamin Davies
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - J D Gantz
- Department of Biology, Miami University, Oxford, OH, USA
- Department of Biology and Health Science, Hendrix College, Conway, AR, USA
| | - Drew E Spacht
- Departments of Entomology and Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kennan Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Souvik Chakraborty
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Richard E Lee
- Department of Biology, Miami University, Oxford, OH, USA
| | - David L Denlinger
- Departments of Entomology and Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Stephen F Matter
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, 95616, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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12
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Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Vargas Jentzsch IM, Oliver JE, Poelchau MF, Rajarapu SP, Schneweis DJ, Snoeck S, Taning CNT, Wei D, Widana Gamage SMK, Hughes DST, Murali SC, Bailey ST, Bejerman NE, Holmes CJ, Jennings EC, Rosendale AJ, Rosselot A, Hervey K, Schneweis BA, Cheng S, Childers C, Simão FA, Dietzgen RG, Chao H, Dinh H, Doddapaneni HV, Dugan S, Han Y, Lee SL, Muzny DM, Qu J, Worley KC, Benoit JB, Friedrich M, Jones JW, Panfilio KA, Park Y, Robertson HM, Smagghe G, Ullman DE, van der Zee M, Van Leeuwen T, Veenstra JA, Waterhouse RM, Weirauch MT, Werren JH, Whitfield AE, Zdobnov EM, Gibbs RA, Richards S. Genome-enabled insights into the biology of thrips as crop pests. BMC Biol 2020; 18:142. [PMID: 33070780 PMCID: PMC7570057 DOI: 10.1186/s12915-020-00862-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
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Affiliation(s)
- Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Aaron A Baumann
- Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA
| | - Sulley Ben-Mahmoud
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Panagiotis Ioannidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Vassilika Vouton, 70013, Heraklion, Greece.,Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Jonathan E Oliver
- Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA
| | | | - Swapna Priya Rajarapu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Derek J Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Simon Snoeck
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Department of Biology, University of Washington, Seattle, WA, 98105, USA
| | - Clauvis N T Taning
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dong Wei
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | | | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | | | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.,Department of Biology, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Andrew Rosselot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Kaylee Hervey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brandi A Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | | | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.,School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | - Diane E Ullman
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | | | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Jan A Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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13
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Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, Chen M, Cheng S, Childers C, Dinh H, Doddapaneni HV, Dugan S, Elpidina EN, Farrow DW, Friedrich M, Gibbs RA, Hall B, Han Y, Hardy RW, Holmes CJ, Hughes DST, Ioannidis P, Cheatle Jarvela AM, Johnston JS, Jones JW, Kronmiller BA, Kung F, Lee SL, Martynov AG, Masterson P, Maumus F, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Nelson DR, Oppert B, Panfilio KA, Paula DP, Pick L, Poelchau MF, Qu J, Reding K, Rhoades JH, Rhodes A, Richards S, Richter R, Robertson HM, Rosendale AJ, Tu ZJ, Velamuri AS, Waterhouse RM, Weirauch MT, Wells JT, Werren JH, Worley KC, Zdobnov EM, Gundersen-Rindal DE. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics 2020; 21:227. [PMID: 32171258 PMCID: PMC7071726 DOI: 10.1186/s12864-020-6510-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/20/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies. RESULTS Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. CONCLUSIONS Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
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Affiliation(s)
- Michael E Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD, 20705, USA.
| | - Raman Bansal
- USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Michael B Blackburn
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD, 20705, USA
| | - Hsu Chao
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mengyao Chen
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | | | - Huyen Dinh
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shannon Dugan
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119911, Russia
| | - David W Farrow
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Richard A Gibbs
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brantley Hall
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Yi Han
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard W Hardy
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Daniel S T Hughes
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
- Present address: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 73100, Heraklion, Crete, Greece
| | | | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Brent A Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Faith Kung
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Sandra L Lee
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alexander G Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Monica Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Shwetha C Murali
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Donna M Muzny
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Brenda Oppert
- USDA-ARS Center for Grain and Animal Health Research, Manhattan, KS, 66502, USA
| | - Kristen A Panfilio
- Developmental Biology, Institute for Zoology: University of Cologne, 50674, Cologne, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, United Kingdom
| | - Débora Pires Paula
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF, 70770-901, Brazil
| | - Leslie Pick
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | | | - Jiaxin Qu
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Katie Reding
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Joshua H Rhoades
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD, 20705, USA
| | - Adelaide Rhodes
- Larner College of Medicine, The University of Vermont, Burlington, VT, 05452, USA
| | - Stephen Richards
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Present address: Earth BioGenome Project, University of California, Davis, Davis, CA, 95616, USA
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Zhijian Jake Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Arun S Velamuri
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD, 20705, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Division of Biomedical Informatics, and Division of Developmental Biology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Jackson T Wells
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Kim C Worley
- Department of Human and Molecular Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
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14
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Rosendale AJ, Dunlevy ME, McCue MD, Benoit JB. Progressive behavioural, physiological and transcriptomic shifts over the course of prolonged starvation in ticks. Mol Ecol 2019; 28:49-65. [PMID: 30449039 DOI: 10.1111/mec.14949] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/29/2018] [Accepted: 07/05/2018] [Indexed: 01/15/2023]
Abstract
Ticks are obligatorily hematophagous but spend the majority of their lives off host in an unfed state where they must resist starvation between bouts of blood feeding. Survival during these extended off-host periods is critical to the success of these arthropods as vectors of disease; however, little is known about the underlying physiological and molecular mechanisms of starvation tolerance in ticks. We examined the bioenergetic, transcriptomic and behavioural changes of female American dog ticks, Dermacentor variabilis, throughout starvation (up to nine months post-bloodmeal). As starvation progressed, ticks utilized glycogen and lipid, and later protein as energy reserves with proteolysis and autophagy facilitating the mobilization of endogenous nutrients. The metabolic rate of the ticks was expectedly low, but showed a slight increase as starvation progressed possibly reflecting the upregulation of several energetically costly processes such as transcription/translation and/or increases in host-seeking behaviours. Starved ticks had higher activity levels, increased questing behaviour and augmented expression of genes related to chemosensing, immunity and salivary gland proteins. The shifts in gene expression and associated behavioural and physiological processes are critical to allowing these parasites to exploit their ecological niche as extreme sit-and-wait parasites. The overall responses of ticks to starvation were similar to other blood-feeding arthropods, but we identified unique responses that could have epidemiological and ecological significance for ticks as ectoparasites that must be tolerant of sporadic feeding.
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Affiliation(s)
- Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Megan E Dunlevy
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | | | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
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15
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Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biol 2019; 20:187. [PMID: 31477173 PMCID: PMC6721284 DOI: 10.1186/s13059-019-1768-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. RESULTS Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. CONCLUSIONS Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
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Affiliation(s)
- Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, USA.
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Alvaro Acosta-Serrano
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - James E Allen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosemary Bateta
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Jelle Caers
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Mikkel B Christensen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - David W Farrow
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Aurélie Hua-Van
- Laboratoire Evolution, Genomes, Comportement, Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Daniel Lawson
- Department of Life Sciences, Imperial College London, London, UK
| | - Michael J Lehane
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Vasileios P Lenis
- Schools of Medicine and Dentistry, University of Plymouth, Plymouth, UK
| | - Ernesto Lowy-Gallego
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosaline W Macharia
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya.,Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Daniel Masiga
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya
| | - Gareth L Maslen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Irina Matetovici
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Irene Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Veronika Michalkova
- Department of Biological Sciences, Florida International University, Miami, Florida, USA.,Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Wolfgang J Miller
- Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul O Mireji
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya.,Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Lino Ometto
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy.,Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Andrew G Parker
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Rita Rio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Clair Rose
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Andrew J Rosendale
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, USA.,Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Omar Rota-Stabelli
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Liliane Schoofs
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Peter Takáč
- Department of Animal Systematics, Ústav zoológie SAV; Scientica, Ltd, Bratislava, Slovakia
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Etoloakarnania, Greece
| | | | - Aurelien Vigneron
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Jingwen Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology & Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Brian L Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Xin Zhao
- CAS Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, China
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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16
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Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biol 2019; 20:187. [PMID: 31477173 DOI: 10.1101/531749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/22/2019] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. RESULTS Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. CONCLUSIONS Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
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Affiliation(s)
- Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, USA.
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Alvaro Acosta-Serrano
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - James E Allen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosemary Bateta
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Jelle Caers
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Mikkel B Christensen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - David W Farrow
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Aurélie Hua-Van
- Laboratoire Evolution, Genomes, Comportement, Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Daniel Lawson
- Department of Life Sciences, Imperial College London, London, UK
| | - Michael J Lehane
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Vasileios P Lenis
- Schools of Medicine and Dentistry, University of Plymouth, Plymouth, UK
| | - Ernesto Lowy-Gallego
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosaline W Macharia
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Daniel Masiga
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya
| | - Gareth L Maslen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Irina Matetovici
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Irene Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Veronika Michalkova
- Department of Biological Sciences, Florida International University, Miami, Florida, USA
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Wolfgang J Miller
- Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul O Mireji
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Lino Ometto
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Andrew G Parker
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Rita Rio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Clair Rose
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Andrew J Rosendale
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, USA
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Omar Rota-Stabelli
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Liliane Schoofs
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Peter Takáč
- Department of Animal Systematics, Ústav zoológie SAV; Scientica, Ltd, Bratislava, Slovakia
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Etoloakarnania, Greece
| | | | - Aurelien Vigneron
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Jingwen Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology & Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Brian L Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Xin Zhao
- CAS Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, China
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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17
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019. [PMID: 30935422 DOI: 10.1101/201731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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18
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019; 20:64. [PMID: 30935422 PMCID: PMC6444547 DOI: 10.1186/s13059-019-1660-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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19
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Armisén D, Rajakumar R, Friedrich M, Benoit JB, Robertson HM, Panfilio KA, Ahn SJ, Poelchau MF, Chao H, Dinh H, Doddapaneni HV, Dugan S, Gibbs RA, Hughes DST, Han Y, Lee SL, Murali SC, Muzny DM, Qu J, Worley KC, Munoz-Torres M, Abouheif E, Bonneton F, Chen T, Chiang LM, Childers CP, Cridge AG, Crumière AJJ, Decaras A, Didion EM, Duncan EJ, Elpidina EN, Favé MJ, Finet C, Jacobs CGC, Cheatle Jarvela AM, Jennings EC, Jones JW, Lesoway MP, Lovegrove MR, Martynov A, Oppert B, Lillico-Ouachour A, Rajakumar A, Refki PN, Rosendale AJ, Santos ME, Toubiana W, van der Zee M, Vargas Jentzsch IM, Lowman AV, Viala S, Richards S, Khila A. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water. BMC Genomics 2018; 19:832. [PMID: 30463532 PMCID: PMC6249893 DOI: 10.1186/s12864-018-5163-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/14/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. RESULTS Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. CONCLUSIONS Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders.
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Affiliation(s)
- David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Rajendhran Rajakumar
- Department of Molecular Genetics & Microbiology and UF Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL 32610-3610 USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Joshua B. Benoit
- Department of Biological Sciences, McMicken College of Arts and Sciences, University of Cincinnati, 318 College Drive, Cincinnati, OH 45221-0006 USA
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Kristen A. Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL UK
| | - Seung-Joon Ahn
- USDA-ARS Horticultural Crops Research Unit, 3420 NW Orchard Avenue, Corvallis, OR 97330 USA
- Department of Crop and Soil Science, Oregon State University, 3050 SW Campus Way, Corvallis, OR 97331 USA
| | - Monica F. Poelchau
- USDA Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Daniel S. T. Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Sandra L. Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Shwetha C. Murali
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Kim C. Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | | | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield Avenue, Montréal, Québec H3A 1B1 Canada
| | - François Bonneton
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Travis Chen
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield Avenue, Montréal, Québec H3A 1B1 Canada
| | - Li-Mei Chiang
- USDA Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
| | | | - Andrew G. Cridge
- Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Antonin J. J. Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Amelie Decaras
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Elise M. Didion
- Department of Biological Sciences, McMicken College of Arts and Sciences, University of Cincinnati, 318 College Drive, Cincinnati, OH 45221-0006 USA
| | - Elizabeth J. Duncan
- Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT UK
| | - Elena N. Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991 Russia
| | - Marie-Julie Favé
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield Avenue, Montréal, Québec H3A 1B1 Canada
| | - Cédric Finet
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Chris G. C. Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745 Jena, Germany
| | | | - Emily C. Jennings
- Department of Biological Sciences, McMicken College of Arts and Sciences, University of Cincinnati, 318 College Drive, Cincinnati, OH 45221-0006 USA
| | - Jeffery W. Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Maryna P. Lesoway
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield Avenue, Montréal, Québec H3A 1B1 Canada
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama City, Panama
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Russia
| | - Mackenzie R. Lovegrove
- Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Alexander Martynov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143025 Russia
| | - Brenda Oppert
- USDA ARS Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS-66502 USA
| | - Angelica Lillico-Ouachour
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield Avenue, Montréal, Québec H3A 1B1 Canada
| | - Arjuna Rajakumar
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield Avenue, Montréal, Québec H3A 1B1 Canada
| | - Peter Nagui Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Andrew J. Rosendale
- Department of Biological Sciences, McMicken College of Arts and Sciences, University of Cincinnati, 318 College Drive, Cincinnati, OH 45221-0006 USA
| | - Maria Emilia Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - William Toubiana
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Iris M. Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Aidamalia Vargas Lowman
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Severine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon 46, allée d’Italie, 69364 Lyon Cedex 07, France
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20
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Meibers HE, Finch G, Gregg RT, Glenn S, Assani KD, Jennings EC, Davies B, Rosendale AJ, Holmes CJ, Gantz JD, Spacht DE, Lee RE, Denlinger DL, Weirauch MT, Benoit JB. Sex- and developmental-specific transcriptomic analyses of the Antarctic mite, Alaskozetes antarcticus, reveal transcriptional shifts underlying oribatid mite reproduction. Polar Biol 2018. [DOI: 10.1007/s00300-018-2427-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuña H, Chen MJM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. Environ Sci Technol 2018; 52:6009-6022. [PMID: 29634279 DOI: 10.15482/usda.adc/1415994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.
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Affiliation(s)
- Helen C Poynton
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Simone Hasenbein
- Aquatic Systems Biology Unit , Technical University of Munich , D-85354 Freising , Germany
| | - Joshua B Benoit
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Maria S Sepulveda
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Monica F Poelchau
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Daniel S T Hughes
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shwetha C Murali
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shuai Chen
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
- OmicSoft Corporation, Cary , North Carolina 27513 United States
| | - Karl M Glastad
- Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 United States
| | - Michael A D Goodisman
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 United States
| | - John H Werren
- Biology Department , University of Rochester , Rochester , New York 14627 United States
| | - Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Markus Friedrich
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Jeffery Jones
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Hugh M Robertson
- Department of Entomology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 United States
| | - René Feyereisen
- Department of Plant and Environmental Sciences , University of Copenhagen , DK-1871 Frederiksberg , Denmark
| | - Alexandra Mechler-Hickson
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Nicholas Mathers
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Carol Eunmi Lee
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - John K Colbourne
- School of Biosciences , University of Birmingham , Birmingham B15 2TT U.K
| | - Adam Biales
- National Exposure Research Laboratory , United States Environmental Protection Agency , Cincinnati , Ohio 45268 United States
| | - J Spencer Johnston
- Department of Entomology , Texas A&M University , College Station , Texas 77843 United States
| | - Gary A Wellborn
- Department of Biology , University of Oklahoma , Norman , Oklahoma 73019 United States
| | - Andrew J Rosendale
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Department of Biochemistry , University of Otago , Dunedin , 9054 New Zealand
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 United States
| | - Peter A Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Urrbrae SA 5064 Australia
| | - Austin R Manny
- Department of Microbiology & Cell Science , University of Florida , Gainesville , Florida 32611 United States
| | - Kaley M Major
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Faith N Lambert
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Chris D Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Padrig Tuck
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Bonnie J Blalock
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Yu-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Mark E Smith
- McConnell Group, Cincinnati , Ohio 45268 , United States
| | - Hugo Ochoa-Acuña
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Christopher P Childers
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Jiaxin Qu
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shannon Dugan
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Sandra L Lee
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Hsu Chao
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Huyen Dinh
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Yi Han
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | | | - Kim C Worley
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
- Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Donna M Muzny
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Richard A Gibbs
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Stephen Richards
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
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22
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Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuña H, Chen MJM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. Environ Sci Technol 2018; 52:6009-6022. [PMID: 29634279 PMCID: PMC6091588 DOI: 10.1021/acs.est.8b00837] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.
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Affiliation(s)
- Helen C Poynton
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Simone Hasenbein
- Aquatic Systems Biology Unit , Technical University of Munich , D-85354 Freising , Germany
| | - Joshua B Benoit
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Maria S Sepulveda
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Monica F Poelchau
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Daniel S T Hughes
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shwetha C Murali
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shuai Chen
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
- OmicSoft Corporation, Cary , North Carolina 27513 United States
| | - Karl M Glastad
- Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 United States
| | - Michael A D Goodisman
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 United States
| | - John H Werren
- Biology Department , University of Rochester , Rochester , New York 14627 United States
| | - Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Markus Friedrich
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Jeffery Jones
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Hugh M Robertson
- Department of Entomology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 United States
| | - René Feyereisen
- Department of Plant and Environmental Sciences , University of Copenhagen , DK-1871 Frederiksberg , Denmark
| | - Alexandra Mechler-Hickson
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Nicholas Mathers
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Carol Eunmi Lee
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - John K Colbourne
- School of Biosciences , University of Birmingham , Birmingham B15 2TT U.K
| | - Adam Biales
- National Exposure Research Laboratory , United States Environmental Protection Agency , Cincinnati , Ohio 45268 United States
| | - J Spencer Johnston
- Department of Entomology , Texas A&M University , College Station , Texas 77843 United States
| | - Gary A Wellborn
- Department of Biology , University of Oklahoma , Norman , Oklahoma 73019 United States
| | - Andrew J Rosendale
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Department of Biochemistry , University of Otago , Dunedin , 9054 New Zealand
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 United States
| | - Peter A Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Urrbrae SA 5064 Australia
| | - Austin R Manny
- Department of Microbiology & Cell Science , University of Florida , Gainesville , Florida 32611 United States
| | - Kaley M Major
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Faith N Lambert
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Chris D Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Padrig Tuck
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Bonnie J Blalock
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Yu-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Mark E Smith
- McConnell Group, Cincinnati , Ohio 45268 , United States
| | - Hugo Ochoa-Acuña
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Christopher P Childers
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Jiaxin Qu
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shannon Dugan
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Sandra L Lee
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Hsu Chao
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Huyen Dinh
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Yi Han
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | | | - Kim C Worley
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
- Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Donna M Muzny
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Richard A Gibbs
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Stephen Richards
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
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23
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Schoville SD, Chen YH, Andersson MN, Benoit JB, Bhandari A, Bowsher JH, Brevik K, Cappelle K, Chen MJM, Childers AK, Childers C, Christiaens O, Clements J, Didion EM, Elpidina EN, Engsontia P, Friedrich M, García-Robles I, Gibbs RA, Goswami C, Grapputo A, Gruden K, Grynberg M, Henrissat B, Jennings EC, Jones JW, Kalsi M, Khan SA, Kumar A, Li F, Lombard V, Ma X, Martynov A, Miller NJ, Mitchell RF, Munoz-Torres M, Muszewska A, Oppert B, Palli SR, Panfilio KA, Pauchet Y, Perkin LC, Petek M, Poelchau MF, Record É, Rinehart JP, Robertson HM, Rosendale AJ, Ruiz-Arroyo VM, Smagghe G, Szendrei Z, Thomas GWC, Torson AS, Vargas Jentzsch IM, Weirauch MT, Yates AD, Yocum GD, Yoon JS, Richards S. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Sci Rep 2018; 8:1931. [PMID: 29386578 PMCID: PMC5792627 DOI: 10.1038/s41598-018-20154-1] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/13/2018] [Indexed: 01/04/2023] Open
Abstract
The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
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Affiliation(s)
- Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, USA.
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | | | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Anita Bhandari
- Department of Molecular Physiology, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | - Kaat Cappelle
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Mei-Ju M Chen
- USDA-ARS National Agricultural Library, Beltsville, MD, USA
| | - Anna K Childers
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | | | | | - Justin Clements
- Department of Entomology, University of Wisconsin-Madison, Madison, USA
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moskva, Russia
| | - Patamarerk Engsontia
- Department of Biology, Faculty of Science, Prince of Songkla University, Amphoe Hat Yai, Thailand
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chandan Goswami
- National Institute of Science Education and Research, Bhubaneswar, India
| | | | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, King Abdulaziz, Saudi Arabia
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | - Megha Kalsi
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Sher A Khan
- Department of Entomology, Texas A&M University, College Station, USA
| | - Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Fei Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
| | - Xingzhou Ma
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alexander Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nicholas J Miller
- Department of Biology, Illinois Institute of Technology, Chicago, USA
| | - Robert F Mitchell
- Department of Biology, University of Wisconsin-Oshkosh, Oshkosh, USA
| | - Monica Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Brenda Oppert
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | | | - Kristen A Panfilio
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, England, UK
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Lindsey C Perkin
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Éric Record
- INRA, Aix-Marseille Université, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Joseph P Rinehart
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | | | - Guy Smagghe
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Zsofia Szendrei
- Department of Entomology, Michigan State University, East Lansing, USA
| | - Gregg W C Thomas
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, USA
| | - Alex S Torson
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | | | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Ashley D Yates
- Department of Entomology, The Ohio State University, Columbus, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, USA
| | - George D Yocum
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - June-Sun Yoon
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Stephen Richards
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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24
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Holmes CJ, Dobrotka CJ, Farrow DW, Rosendale AJ, Benoit JB, Pekins PJ, Yoder JA. Low and high thermal tolerance characteristics for unfed larvae of the winter tick Dermacentor albipictus (Acari: Ixodidae) with special reference to moose. Ticks Tick Borne Dis 2017; 9:25-30. [PMID: 29103951 DOI: 10.1016/j.ttbdis.2017.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/05/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
We report that larvae of the winter tick Dermacentor albipictus, the only stage that will quest for a host, can tolerate short-term cold shock down to -25°C and short-term heat shock as high as 46°C. Unlike a three host-tick, larvae of D. albipictus have no preconditioning response to low or high temperature exposure by rapid cold hardening (RCH) or heat hardening, and poor ability to acclimate to low and high temperature extremes. Thermal tolerance limits were not improved as the result of larval clustering, and there was only a minimal effect due to changes in photoperiod. These larvae are freeze intolerant and die at higher temperatures (-5 to -10°C) from contact with ice by inoculative freezing. In absence of cold-associated resistance mechanisms, winter survival requires that larvae procure a host before the first snow cover. Their low and high temperature tolerance, however, is a key survival element that adapts them for off-host periods during summer, which in the arctic could allow for northern expansion.
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Affiliation(s)
- Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
| | - Cameron J Dobrotka
- Department of Biology, Wittenberg University, Springfield, OH 45501, USA.
| | - David W Farrow
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
| | - Peter J Pekins
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA.
| | - Jay A Yoder
- Department of Biology, Wittenberg University, Springfield, OH 45501, USA.
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25
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Rosendale AJ, Romick-Rosendale LE, Watanabe M, Dunlevy ME, Benoit JB. Mechanistic underpinnings of dehydration stress in the American dog tick revealed through RNA-Seq and metabolomics. ACTA ACUST UNITED AC 2017; 219:1808-19. [PMID: 27307540 DOI: 10.1242/jeb.137315] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/17/2016] [Indexed: 01/22/2023]
Abstract
Ticks are obligate blood feeders but spend the majority of their lifetime off-host where they must contend with a multitude of environmental stresses. Survival under desiccating conditions is a determinant for habitats where ticks can become established, and water-balance characteristics of ticks have been extensively studied. However, little is known about the underlying aspects associated with dehydration stress in ticks. In this study, we examined the response of male American dog ticks, Dermacentor variabilis, to dehydration using a combined transcriptomics and metabolomics approach. During dehydration, 497 genes were differentially expressed, including an up-regulation of stress-response and protein-catabolism genes and concurrent down-regulation of several energetically expensive biological processes. Accumulation of several metabolites, including specific amino acids, glycerol and gamma aminobutyric acid (GABA), and transcript shifts in the associated pathways for generating these metabolites indicated congruence between changes in the metabolome and gene expression. Ticks treated with exogenous glycerol and GABA demonstrated altered water-balance characteristics; specifically, increased water absorption at high relative humidity. Finally, we observed changes in locomotor activity in response to dehydration, but this change was not influenced by the accumulation of GABA. Overall, the responses to dehydration by these ticks were similar to those observed in other dehydration-tolerant arthropods, but several molecular and behavioral responses are distinct from those associated with other taxa.
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Affiliation(s)
- Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Miki Watanabe
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Megan E Dunlevy
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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26
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Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castañera P, Cavanaugh JP, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, González-Guzmán M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernández-Crespo P, Hughes DST, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu J, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Ureña E, S Vlachos I, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM. Erratum to: The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol 2017; 18:11. [PMID: 28100280 PMCID: PMC5241912 DOI: 10.1186/s13059-017-1155-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/12/2017] [Indexed: 12/03/2022] Open
Affiliation(s)
- Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Marc F Schetelig
- Justus-Liebig-University Giessen, Institute for Insect Biotechnology, 35394, Giessen, Germany
| | - Peter Arensburger
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, 91768, USA
| | - Peter W Atkinson
- Department of Entomology and Center for Disease Vector Research, University of California Riverside, Riverside, CA, 92521, USA.,Interdepartmental Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, CA, 92521, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria.,Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece
| | - Pedro Castañera
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - John P Cavanaugh
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | | | - Ingrid Curril
- Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, 37077, Göttingen, Germany
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, 14627, Rochester, NY, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, 48202, Detroit, MI, USA
| | - Giuliano Gasperi
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Scott Geib
- USDA-ARS, Pacific Basin Agricultural Research Center, 96720, Hilo, HI, USA
| | - Georgios Georgakilas
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Sarah D Giers
- Department of Entomology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
| | - Ludvik M Gomulski
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Miguel González-Guzmán
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Ana Guillem-Amat
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Pedro Hernández-Crespo
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, 48309, Rochester, MI, USA
| | - Dimitra Karagkouni
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Panagiota Koskinioti
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Mosè Manni
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Kostas Mathiopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Angela Meccariello
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Monica Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20892, Bethesda, MD, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Georg Oberhofer
- Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, 37077, Göttingen, Germany
| | - Félix Ortego
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Maria D Paraskevopoulou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Monica Poelchau
- National Agricultural Library, USDA, 20705, Beltsville, MD, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Martin Reczko
- Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre "Alexander Fleming", Athens, Greece
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew E Rosselot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Giuseppe Saccone
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Patrick Schreiner
- Interdepartmental Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, CA, 92521, USA
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Paolo Siciliano
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Sheina B Sim
- USDA-ARS, Pacific Basin Agricultural Research Center, 96720, Hilo, HI, USA
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece
| | - Enric Ureña
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Ioannis S Vlachos
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - John H Werren
- Department of Biology, University of Rochester, 14627, Rochester, NY, USA
| | - Ernst A Wimmer
- Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, 37077, Göttingen, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | | | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, 77030, Houston, TX, USA
| | - Alfred M Handler
- USDA-ARS, Center for Medical, Agricultural and Veterinary Entomology, 1700 S.W. 23rd Drive, Gainesville, FL, 32608, USA.
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27
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McKenna DD, Scully ED, Pauchet Y, Hoover K, Kirsch R, Geib SM, Mitchell RF, Waterhouse RM, Ahn SJ, Arsala D, Benoit JB, Blackmon H, Bledsoe T, Bowsher JH, Busch A, Calla B, Chao H, Childers AK, Childers C, Clarke DJ, Cohen L, Demuth JP, Dinh H, Doddapaneni H, Dolan A, Duan JJ, Dugan S, Friedrich M, Glastad KM, Goodisman MAD, Haddad S, Han Y, Hughes DST, Ioannidis P, Johnston JS, Jones JW, Kuhn LA, Lance DR, Lee CY, Lee SL, Lin H, Lynch JA, Moczek AP, Murali SC, Muzny DM, Nelson DR, Palli SR, Panfilio KA, Pers D, Poelchau MF, Quan H, Qu J, Ray AM, Rinehart JP, Robertson HM, Roehrdanz R, Rosendale AJ, Shin S, Silva C, Torson AS, Jentzsch IMV, Werren JH, Worley KC, Yocum G, Zdobnov EM, Gibbs RA, Richards S. Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. Genome Biol 2016; 17:227. [PMID: 27832824 PMCID: PMC5105290 DOI: 10.1186/s13059-016-1088-8] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/19/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle. RESULTS The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates. CONCLUSIONS Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.
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Affiliation(s)
- Duane D. McKenna
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
- Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152 USA
| | - Erin D. Scully
- USDA, Agricultural Research Service, Center for Grain and Animal Health, Stored Product Insect and Engineering Research Unit, Manhattan, KS 66502 USA
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Kelli Hoover
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Scott M. Geib
- USDA, Agricultural Research Service, Daniel K Inouye US Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, Hilo, HI 96720 USA
| | - Robert F. Mitchell
- Center for Insect Science and Department of Neuroscience, University of Arizona, Tucson, AZ 85721 USA
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901 USA
| | - Robert M. Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, Geneva, 1211 Switzerland
- The Massachusetts Institute of Technology and The Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Deanna Arsala
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Heath Blackmon
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019 USA
| | - Tiffany Bledsoe
- Center for Insect Science and Department of Neuroscience, University of Arizona, Tucson, AZ 85721 USA
| | - Julia H. Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58108 USA
| | - André Busch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Bernarda Calla
- USDA, Agricultural Research Service, Daniel K Inouye US Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, Hilo, HI 96720 USA
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Anna K. Childers
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Christopher Childers
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
| | - Dave J. Clarke
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
| | - Lorna Cohen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Jeffery P. Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019 USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Jian J. Duan
- USDA, Agricultural Research Service, Beneficial Insects Introduction Research, Newark, DE 19713 USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Karl M. Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | | | - Stephanie Haddad
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Daniel S. T. Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, Geneva, 1211 Switzerland
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843 USA
| | - Jeffery W. Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Leslie A. Kuhn
- Department of Biochemistry and Molecular Biology, Department of Computers Science and Engineering, and Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824 USA
| | - David R. Lance
- USDA, Animal and Plant Health Inspection Service, Plant Pest and Quarantine, Center for Plant Health Science and Technology, Otis Laboratory, Buzzards Bay, MA 02542 USA
| | - Chien-Yueh Lee
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617 Taiwan
| | - Sandra L. Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Han Lin
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617 Taiwan
| | - Jeremy A. Lynch
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Armin P. Moczek
- Department of Biology, Indiana University, Blomington, IN 47405 USA
| | - Shwetha C. Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - David R. Nelson
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163 USA
| | - Subba R. Palli
- Department of Entomology, University of Kentucky, Lexington, KY 40546 USA
| | - Kristen A. Panfilio
- Institute for Developmental Biology, University of Cologne, Cologne, 50674 Germany
| | - Dan Pers
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Monica F. Poelchau
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
| | - Honghu Quan
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Ann M. Ray
- Department of Biology, Xavier University, Cincinnati, OH 45207 USA
| | - Joseph P. Rinehart
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Richard Roehrdanz
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Andrew J. Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
| | - Christian Silva
- Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Alex S. Torson
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58108 USA
| | | | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Kim C. Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - George Yocum
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Evgeny M. Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, Geneva, 1211 Switzerland
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castañera P, Cavanaugh JP, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, González-Guzmán M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernández-Crespo P, Hughes DST, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu J, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Ureña E, Vlachos IS, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM. The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol 2016; 17:192. [PMID: 27659211 PMCID: PMC5034548 DOI: 10.1186/s13059-016-1049-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/26/2016] [Indexed: 01/01/2023] Open
Abstract
Background The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control. Results The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT. Conclusions The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1049-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Marc F Schetelig
- Justus-Liebig-University Giessen, Institute for Insect Biotechnology, 35394, Giessen, Germany
| | - Peter Arensburger
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, 91768, USA
| | - Peter W Atkinson
- Department of Entomology and Center for Disease Vector Research, University of California Riverside, Riverside, CA, 92521, USA.,Interdepartmental Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, CA, 92521, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria.,Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece
| | - Pedro Castañera
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - John P Cavanaugh
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Ingrid Curril
- Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, 37077, Göttingen, Germany
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Giuliano Gasperi
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Scott Geib
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Georgios Georgakilas
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sarah D Giers
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ludvik M Gomulski
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Miguel González-Guzmán
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Ana Guillem-Amat
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Pedro Hernández-Crespo
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
| | - Dimitra Karagkouni
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Panagiota Koskinioti
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Mosè Manni
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Kostas Mathiopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Angela Meccariello
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | | | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Georg Oberhofer
- Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, 37077, Göttingen, Germany
| | - Félix Ortego
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Maria D Paraskevopoulou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Monica Poelchau
- National Agricultural Library, USDA, Beltsville, MD, 20705, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin Reczko
- Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre "Alexander Fleming", Vari, Greece
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew E Rosselot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Giuseppe Saccone
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Patrick Schreiner
- Interdepartmental Graduate Program in Genetics, Genomics & Bioinformatics, University of California Riverside, Riverside, CA, 92521, USA
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Paolo Siciliano
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Sheina B Sim
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece
| | - Enric Ureña
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Ioannis S Vlachos
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece and Hellenic Pasteur Institute, 11521, Athens, Greece
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Ernst A Wimmer
- Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, 37077, Göttingen, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alfred M Handler
- USDA-ARS, Center for Medical, Agricultural, and Veterinary Entomology, 1700 S.W. 23rd Drive, Gainesville, FL, 32608, USA.
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Yoder JA, Rosendale AJ, Benoit JB. Short day-triggered quiescence promotes water conservation in the American dog tick, Dermacentor variabilis. J Comp Physiol B 2015; 186:287-96. [DOI: 10.1007/s00360-015-0955-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/23/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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Rosendale AJ, Lee RE, Costanzo JP. Effect of physiological stress on expression of glucose transporter 2 in liver of the wood frog, Rana sylvatica. ACTA ACUST UNITED AC 2014; 321:566-76. [PMID: 25384572 DOI: 10.1002/jez.1885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/18/2014] [Accepted: 07/28/2014] [Indexed: 11/11/2022]
Abstract
Glucose transporters (GLUTs) have been implicated in the survival of various physiological stresses in mammals; however, little is known about the role of these proteins in stress tolerance in lower vertebrates. The wood frog (Rana sylvatica), which survives multiple winter-related stresses by copiously mobilizing hepatic glycogen stores, is an interesting subject for the study of glucose transport in amphibians. We examined the effects of several physiological stresses on GLUT2 protein and mRNA levels in the liver of R. sylvatica. Using immunoblotting techniques to measure relative GLUT2 abundance, we found that GLUT2 numbers increased in response to organismal freezing, hypoxia exposure, and glucose loading; whereas, experimental dehydration and urea loading did not affect GLUT2 abundance. GLUT2 mRNA levels, assessed using quantitative real-time polymerase chain reaction, changed in accordance with protein abundance for most stresses, indicating that transcriptional regulation of GLUT2 occurs in response to stress. Overall, hepatic GLUT2 seems to be important in stress survival in R. sylvatica and is regulated to meet the physiological need to accumulate glucose.
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Rosendale AJ, Philip BN, Lee RE, Costanzo JP. Cloning, characterization, and expression of glucose transporter 2 in the freeze-tolerant wood frog, Rana sylvatica. Biochim Biophys Acta Gen Subj 2014; 1840:1701-11. [DOI: 10.1016/j.bbagen.2013.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 12/01/2013] [Accepted: 12/09/2013] [Indexed: 01/22/2023]
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Costanzo JP, do Amaral MCF, Rosendale AJ, Lee RE. Hibernation physiology, freezing adaptation and extreme freeze tolerance in a northern population of the wood frog. J Exp Biol 2013; 216:3461-73. [DOI: 10.1242/jeb.089342] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
We investigated hibernation physiology and freeze tolerance in a population of the wood frog, Rana sylvatica, indigenous to Interior Alaska, USA, near the northernmost limit of the species' range. Winter acclimatization responses included a 233% increase in the hepatic glycogen depot that was subsidized by fat body and skeletal muscle catabolism, and a rise in plasma osmolality that reflected accrual of urea (to 106±10 μmol ml−1) and an unidentified solute (to ~73 μmol ml−1). In contrast, frogs from a cool-temperate population (southern Ohio, USA) amassed much less glycogen, had a lower uremia (28±5 μmol ml−1) and apparently lacked the unidentified solute. Alaskan frogs survived freezing at temperatures as low as −16°C, some 10–13°C below those tolerated by southern conspecifics, and endured a 2-month bout of freezing at −4°C. The profound freeze tolerance is presumably due to their high levels of organic osmolytes and bound water, which limits ice formation. Adaptive responses to freezing (−2.5°C for 48 h) and subsequent thawing (4°C) included synthesis of the cryoprotectants urea and glucose, and dehydration of certain tissues. Alaskan frogs differed from Ohioan frogs in retaining a substantial reserve capacity for glucose synthesis, accumulating high levels of cryoprotectants in brain tissue, and remaining hyperglycemic long after thawing. The northern phenotype also incurred less stress during freezing/thawing, as indicated by limited cryohemolysis and lactate accumulation. Post-glacial colonization of high latitudes by R. sylvatica required a substantial increase in freeze tolerance that was at least partly achieved by enhancing their cryoprotectant system.
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Affiliation(s)
- Jon P. Costanzo
- Department of Zoology, Miami University, Oxford, OH 45056, USA
| | | | | | - Richard E. Lee
- Department of Zoology, Miami University, Oxford, OH 45056, USA
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33
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Rosendale AJ, Costanzo JP, Lee RE. Seasonal variation and response to osmotic challenge in urea transporter expression in the dehydration- and freeze-tolerant wood frog, Rana sylvatica. J Exp Zool A Ecol Genet Physiol 2012; 317:401-9. [PMID: 22639427 DOI: 10.1002/jez.1733] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 03/20/2012] [Accepted: 04/03/2012] [Indexed: 11/09/2022]
Abstract
Urea accumulation is a universal response to osmotic challenge in anuran amphibians, and facilitative urea transporters (UTs) seem to play an important role in this process by acting in the osmoregulatory organs to mediate urea retention. Although UTs have been implicated in urea reabsorption in anurans, little is known about the physiological regulation of UT protein abundance. We examined seasonal variation in and effects of osmotic challenge on UT protein and mRNA levels in kidney and urinary bladder of the wood frog (Rana sylvatica), a terrestrial species that tolerates both dehydration and tissue freezing. Using immunoblotting techniques to measure relative UT abundance, we found that UT numbers varied seasonally, with a low abundance prevailing in the fall and winter, and higher levels occurring in the spring. Experimental dehydration of frogs increased UT protein abundance in the urinary bladder, whereas experimental urea loading decreased the abundance of UTs in kidney and bladder. Experimental freezing, whether or not followed by thawing, had no effect on UT numbers. UT mRNA levels, assessed using quantitative real-time polymerase chain reaction, did not change seasonally nor in response to any of our experimental treatments. These findings suggest that regulation of UTs depends on the nature and severity of the osmotic stress and apparently occurs posttranscriptionally in response to multiple physiological factors. Additionally, UTs seem to be regulated to meet the physiological need to accumulate urea, with UT numbers increasing to facilitate urea reabsorption and decreasing to prevent retention of excess urea.
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