1
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Damayo JE, McKee RC, Buchmann G, Norton AM, Ashe A, Remnant EJ. Virus replication in the honey bee parasite, Varroa destructor. J Virol 2023; 97:e0114923. [PMID: 37966226 PMCID: PMC10746231 DOI: 10.1128/jvi.01149-23] [Citation(s) in RCA: 1] [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: 07/26/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The parasitic mite Varroa destructor is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee Apis mellifera. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in V. destructor demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.
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Affiliation(s)
- James E. Damayo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca C. McKee
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gabriele Buchmann
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Institute of Plant Genetics, Heinrich-Heine University, Duesseldorf, Germany
| | - Amanda M. Norton
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Academic Support Unit, Research and Advanced Instrumentation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Emily J. Remnant
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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2
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Chapman NC, Colin T, Cook J, da Silva CRB, Gloag R, Hogendoorn K, Howard SR, Remnant EJ, Roberts JMK, Tierney SM, Wilson RS, Mikheyev AS. The final frontier: ecological and evolutionary dynamics of a global parasite invasion. Biol Lett 2023; 19:20220589. [PMID: 37222245 PMCID: PMC10207324 DOI: 10.1098/rsbl.2022.0589] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/11/2022] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Studying rapid biological changes accompanying the introduction of alien organisms into native ecosystems can provide insights into fundamental ecological and evolutionary theory. While powerful, this quasi-experimental approach is difficult to implement because the timing of invasions and their consequences are hard to predict, meaning that baseline pre-invasion data are often missing. Exceptionally, the eventual arrival of Varroa destructor (hereafter Varroa) in Australia has been predicted for decades. Varroa is a major driver of honeybee declines worldwide, particularly as vectors of diverse RNA viruses. The detection of Varroa in 2022 at over a hundred sites poses a risk of further spread across the continent. At the same time, careful study of Varroa's spread, if it does become established, can provide a wealth of information that can fill knowledge gaps about its effects worldwide. This includes how Varroa affects honeybee populations and pollination. Even more generally, Varroa invasion can serve as a model for evolution, virology and ecological interactions between the parasite, the host and other organisms.
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Affiliation(s)
- Nadine C. Chapman
- School of Life and Environmental Sciences, Behaviour, Ecology and Evolution Lab, The University of Sydney, NSW 2006, Australia
| | - Théotime Colin
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - James Cook
- Hawkesbury Institute for the Environment, Western Sydney University, NSW 2753, Australia
| | - Carmen R. B. da Silva
- School of Biological Sciences, Faculty of Science, Monash University, Clayton Victoria 3800, Australia
| | - Ros Gloag
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Katja Hogendoorn
- School of Agriculture, The University of Adelaide, Food and Wine, Adelaide SA 5005, Australia
| | - Scarlett R. Howard
- Hawkesbury Institute for the Environment, Western Sydney University, NSW 2753, Australia
| | - Emily J. Remnant
- School of Life and Environmental Sciences, Behaviour, Ecology and Evolution Lab, The University of Sydney, NSW 2006, Australia
| | - John M. K. Roberts
- Commonwealth Scientific & Industrial Research Organisation, Canberra 2601, ACT, Australia
| | - Simon M. Tierney
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, USA
| | - Rachele S. Wilson
- School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Alexander S. Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT 26000, Australia
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3
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Fernandes KE, Frost EA, Remnant EJ, Schell KR, Cokcetin NN, Carter DA. The role of honey in the ecology of the hive: Nutrition, detoxification, longevity, and protection against hive pathogens. Front Nutr 2022; 9:954170. [PMID: 35958247 PMCID: PMC9359632 DOI: 10.3389/fnut.2022.954170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Honey is the source of energy for the European honey bee, Apis mellifera. Beyond simple nutrition and a hedge against the seasonal, geographic, and chemical unpredictability of nectar, honey has properties that protect the hive against various stresses. Enzyme-mediated detoxification during honey ripening neutralizes potentially toxic phytochemicals, and bees that consume honey have enhanced tolerance to other ingested toxins. Catalase and antioxidant phenolics protect honey bees from oxidative damage caused by reactive oxygen species, promoting their longevity. Phytochemical components of honey and microRNAs have the potential to influence developmental pathways, with diet playing a large role in honey bee caste determination. Components of honey mediate stress response and promote cold tolerance during overwintering. Honey has a suite of antimicrobial mechanisms including osmotic pressure, low water activity, low pH, hydrogen peroxide, and plant-, honey bee-, and microbiota-derived compounds such as phytochemicals and antimicrobial peptides. Certain types of honey, particularly polyfloral honeys, have been shown to inhibit important honey bee pathogens including the bacteria responsible for American and European Foulbrood, the microsporidian Nosema ceranae, and the fungi responsible for Stonebrood. Understanding the diverse functional properties of honey has far-ranging implications for honey bee and hive health and management by beekeepers.
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Affiliation(s)
- Kenya E Fernandes
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Elizabeth A Frost
- Animal Genetics & Breeding Unit (ABGU), A Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW, Australia.,NSW Department of Primary Industries, Paterson, NSW, Australia
| | - Emily J Remnant
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Kathleen R Schell
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, NSW, Australia
| | - Nural N Cokcetin
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, NSW, Australia
| | - Dee A Carter
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia
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4
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Lester PJ, Felden A, Baty JW, Bulgarella M, Haywood J, Mortensen AN, Remnant EJ, Smeele ZE. Viral communities in the parasite Varroa destructor and in colonies of their honey bee host (Apis mellifera) in New Zealand. Sci Rep 2022; 12:8809. [PMID: 35614309 PMCID: PMC9133037 DOI: 10.1038/s41598-022-12888-w] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/11/2022] [Indexed: 11/11/2022] Open
Abstract
The parasitic mite Varroa destructor is a leading cause of mortality for Western honey bee (Apis mellifera) colonies around the globe. We sought to confirm the presence and likely introduction of only one V. destructor haplotype in New Zealand, and describe the viral community within both V. destructor mites and the bees that they parasitise. A 1232 bp fragment from mitochondrial gene regions suggests the likely introduction of only one V. destructor haplotype to New Zealand. Seventeen viruses were found in bees. The most prevalent and abundant was the Deformed wing virus A (DWV-A) strain, which explained 95.0% of the variation in the viral community of bees. Black queen cell virus, Sacbrood virus, and Varroa destructor virus 2 (VDV-2) played secondary roles. DWV-B and the Israeli acute paralysis virus appeared absent from New Zealand. Ten viruses were observed in V. destructor, with > 99.9% of viral reads from DWV-A and VDV-2. Substantially more variation in viral loads was observed in bees compared to mites. Where high levels of VDV-2 occurred in mites, reduced DWV-A occurred in both the mites and the bees co-occurring within the same hive. Where there were high loads of DWV-A in mites, there were typically high viral loads in bees.
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Affiliation(s)
- Philip J Lester
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand.
| | - Antoine Felden
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - James W Baty
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - Mariana Bulgarella
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - John Haywood
- School of Mathematics and Statistics, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - Ashley N Mortensen
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 3230, Waikato Mail Centre, Hamilton, 3240, New Zealand
| | - Emily J Remnant
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Science Road, Sydney, NSW, 2006, Australia
| | - Zoe E Smeele
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
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5
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Watson OT, Buchmann G, Young P, Lo K, Remnant EJ, Yagound B, Shambrook M, Hill AF, Oldroyd BP, Ashe A. Abundant small RNAs in the reproductive tissues and eggs of the honey bee, Apis mellifera. BMC Genomics 2022; 23:257. [PMID: 35379185 PMCID: PMC8978429 DOI: 10.1186/s12864-022-08478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Background Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Results Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in the semen of other animals. Intriguingly we also find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. Conclusions We conclude that small RNAs may play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of-origin effects on gene expression and reproductive physiology. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08478-9.
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Affiliation(s)
- Owen T Watson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gabriele Buchmann
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Paul Young
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute NSW 2010, Darlinghurst, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Emily J Remnant
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mitch Shambrook
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Andrew F Hill
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia.,Institute for Health and Sport, Victoria University, Footscray, VIC, Australia
| | - Benjamin P Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia. .,Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193, Berlin, Germany.
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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6
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de Miranda JR, Brettell LE, Chejanovsky N, Childers AK, Dalmon A, Deboutte W, de Graaf DC, Doublet V, Gebremedhn H, Genersch E, Gisder S, Granberg F, Haddad NJ, Kaden R, Manley R, Matthijnssens J, Meeus I, Migdadi H, Milbrath MO, Mondet F, Remnant EJ, Roberts JMK, Ryabov EV, Sela N, Smagghe G, Somanathan H, Wilfert L, Wright ON, Martin SJ, Ball BV. Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt. Virol J 2022; 19:12. [PMID: 35033134 PMCID: PMC8760790 DOI: 10.1186/s12985-022-01740-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 08/04/2021] [Accepted: 12/31/2021] [Indexed: 01/11/2023] Open
Abstract
In 1977, a sample of diseased adult honeybees (Apis mellifera) from Egypt was found to contain large amounts of a previously unknown virus, Egypt bee virus, which was subsequently shown to be serologically related to deformed wing virus (DWV). By sequencing the original isolate, we demonstrate that Egypt bee virus is in fact a fourth unique, major variant of DWV (DWV-D): more closely related to DWV-C than to either DWV-A or DWV-B. DWV-A and DWV-B are the most common DWV variants worldwide due to their close relationship and transmission by Varroa destructor. However, we could not find any trace of DWV-D in several hundred RNA sequencing libraries from a worldwide selection of honeybee, varroa and bumblebee samples. This means that DWV-D has either become extinct, been replaced by other DWV variants better adapted to varroa-mediated transmission, or persists only in a narrow geographic or host range, isolated from common bee and beekeeping trade routes.
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Affiliation(s)
- Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden.
| | - Laura E Brettell
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Renrith, NSW, 2751, Australia.,School of Environment and Life Sciences, University of Salford, Manchester, M5 4WT, UK.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Nor Chejanovsky
- Institute of Plant Protection, The Volcani Center, PO Box 15159, 7528809, Rishon Lezion, Israel
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Anne Dalmon
- Abeilles et Environnement, INRAE, 84914, Avignon, France
| | - Ward Deboutte
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, University of Leuven, 3000, Leuven, Belgium.,Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, 9000, Ghent, Belgium
| | - Vincent Doublet
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Haftom Gebremedhn
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, 9000, Ghent, Belgium.,Tigray Agricultural Research Institute, P.O. Box 492, Mekelle, Ethiopia
| | - Elke Genersch
- Institut Für Mikrobiologie Und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Sebastian Gisder
- Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Fredrik Granberg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden
| | - Nizar J Haddad
- Bee Research Department, National Agricultural Research Center, Baq'a, Jordan
| | - Rene Kaden
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden.,Clinical Microbiology, Department of Medical Sciences, Uppsala University, 753 09, Uppsala, Sweden
| | - Robyn Manley
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK
| | - Jelle Matthijnssens
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, University of Leuven, 3000, Leuven, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Hussein Migdadi
- Bee Research Department, National Agricultural Research Center, Baq'a, Jordan
| | - Meghan O Milbrath
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden
| | - Fanny Mondet
- Abeilles et Environnement, INRAE, 84914, Avignon, France
| | - Emily J Remnant
- Behaviour, Ecology and Evolution (BEE) Lab, School of Life and Environmental Sciences, The University of Sydney, Camperdown, 2006, Australia
| | - John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, 2601, Australia
| | - Eugene V Ryabov
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Noa Sela
- Institute of Plant Protection, The Volcani Center, PO Box 15159, 7528809, Rishon Lezion, Israel
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Hema Somanathan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Lena Wilfert
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Owen N Wright
- Centre for Research in Animal Behaviour, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QG, UK
| | - Stephen J Martin
- School of Environment and Life Sciences, University of Salford, Manchester, M5 4WT, UK.,Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Brenda V Ball
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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Cardoso-Júnior CAM, Yagound B, Ronai I, Remnant EJ, Hartfelder K, Oldroyd BP. DNA methylation is not a driver of gene expression reprogramming in young honey bee workers. Mol Ecol 2021; 30:4804-4818. [PMID: 34322926 DOI: 10.1111/mec.16098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/06/2021] [Accepted: 07/16/2021] [Indexed: 12/01/2022]
Abstract
The presence of DNA methylation marks within genic intervals, also called gene body methylation, is an evolutionarily-conserved epigenetic hallmark of animal and plant methylomes. In social insects, gene body methylation is thought to contribute to behavioural plasticity, for example between foragers and nurse workers, by modulating gene expression. However, recent studies have suggested that the majority of DNA methylation is sequence-specific, and therefore cannot act as a flexible mediator between environmental cues and gene expression. To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen. Although these social contexts are known to bring about extreme changes in behavioral and reproductive traits through differential gene expression, we found no significant differences between the methylomes of workers from queenright and queenless colonies. In contrast, thousands of regions were differentially methylated between colonies, and these differences were not associated with differential gene expression in the subset of genes examined. Methylation patterns were highly similar between brain and ovary tissues and only differed in nine regions. These results strongly indicate that DNA methylation is not a driver of differential gene expression between tissues or behavioral morphs. Finally, despite the lack of difference in methylation patterns, queen presence affected the expression of all four DNA methyltransferase genes, suggesting that these enzymes have roles beyond DNA methylation. Therefore, the functional role of DNA methylation in social insect genomes remains an open question.
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Affiliation(s)
- Carlos A M Cardoso-Júnior
- Departamento de Biologia Celular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil.,Behaviour, Ecology and Evolution (BEE) Laboratory, Ecology and Evolution, School of Life and Environmental Sciences A12, University of Sydney, Sydney, NSW, Australia
| | - Boris Yagound
- Behaviour, Ecology and Evolution (BEE) Laboratory, Ecology and Evolution, School of Life and Environmental Sciences A12, University of Sydney, Sydney, NSW, Australia
| | - Isobel Ronai
- Behaviour, Ecology and Evolution (BEE) Laboratory, Ecology and Evolution, School of Life and Environmental Sciences A12, University of Sydney, Sydney, NSW, Australia
| | - Emily J Remnant
- Behaviour, Ecology and Evolution (BEE) Laboratory, Ecology and Evolution, School of Life and Environmental Sciences A12, University of Sydney, Sydney, NSW, Australia
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | - Benjamin P Oldroyd
- Behaviour, Ecology and Evolution (BEE) Laboratory, Ecology and Evolution, School of Life and Environmental Sciences A12, University of Sydney, Sydney, NSW, Australia.,Wissenschaftskolleg zu Berlin, Berlin, Germany
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8
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Remnant EJ, Baty JW, Bulgarella M, Dobelmann J, Quinn O, Gruber MAM, Lester PJ. A Diverse Viral Community from Predatory Wasps in Their Native and Invaded Range, with a New Virus Infectious to Honey Bees. Viruses 2021; 13:1431. [PMID: 34452301 PMCID: PMC8402789 DOI: 10.3390/v13081431] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Wasps of the genus Vespula are social insects that have become major pests and predators in their introduced range. Viruses present in these wasps have been studied in the context of spillover from honey bees, yet we lack an understanding of the endogenous virome of wasps as potential reservoirs of novel emerging infectious diseases. We describe the characterization of 68 novel and nine previously identified virus sequences found in transcriptomes of Vespula vulgaris in colonies sampled from their native range (Belgium) and an invasive range (New Zealand). Many viruses present in the samples were from the Picorna-like virus family (38%). We identified one Luteo-like virus, Vespula vulgaris Luteo-like virus 1, present in the three life stages examined in all colonies from both locations, suggesting this virus is a highly prevalent and persistent infection in wasp colonies. Additionally, we identified a novel Iflavirus with similarity to a recently identified Moku virus, a known wasp and honey bee pathogen. Experimental infection of honey bees with this novel Vespula vulgaris Moku-like virus resulted in an active infection. The high viral diversity present in these invasive wasps is a likely indication that their polyphagous diet is a rich source of viral infections.
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Affiliation(s)
- Emily J. Remnant
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, Science Road, University of Sydney, Sydney, NSW 2006, Australia
| | - James W. Baty
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
| | - Mariana Bulgarella
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
| | - Jana Dobelmann
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
- Institute of Evolutionary Ecology and Conservation Genomics, Department of Biology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Oliver Quinn
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
- Bacteriology and Aquatic Animal Diseases, Ministry for Primary Industries, P.O. Box 2526, Wellington 6140, New Zealand
| | - Monica A. M. Gruber
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
| | - Philip J. Lester
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
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9
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Yagound B, Remnant EJ, Buchmann G, Oldroyd BP. Reply to Soley: DNA methylation marks are stably transferred across generations in honey bees. Proc Natl Acad Sci U S A 2021; 118:e2109211118. [PMID: 34260407 PMCID: PMC8285941 DOI: 10.1073/pnas.2109211118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Boris Yagound
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia;
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Emily J Remnant
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Gabriele Buchmann
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Benjamin P Oldroyd
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
- Wissenschaftskolleg zu Berlin, 14193 Berlin, Germany
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Harrop TWR, Guhlin J, McLaughlin GM, Permina E, Stockwell P, Gilligan J, Le Lec MF, Gruber MAM, Quinn O, Lovegrove M, Duncan EJ, Remnant EJ, Eeckhoven JV, Graham B, Knapp RA, Langford KW, Kronenberg Z, Press MO, Eacker SM, Wilson-Rankin EE, Purcell J, Lester PJ, Dearden PK. Corrigendum to “High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus”. G3 Genes|Genomes|Genetics 2021; 11:6262084. [PMID: 34009344 PMCID: PMC8495737 DOI: 10.1093/g3journal/jkab109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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11
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Norton AM, Remnant EJ, Tom J, Buchmann G, Blacquiere T, Beekman M. Adaptation to vector-based transmission in a honeybee virus. J Anim Ecol 2021; 90:2254-2267. [PMID: 33844844 DOI: 10.1111/1365-2656.13493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 09/08/2020] [Accepted: 04/06/2021] [Indexed: 11/27/2022]
Abstract
Global pollinator declines as a result of emerging infectious diseases are of major concern. Managed honeybees Apis mellifera are susceptible to numerous parasites and pathogens, many of which appear to be transmissible to sympatric non-Apis taxa. The ectoparasitic mite Varroa destructor is considered to be the most significant threat to honeybees due to its role in vectoring RNA viruses, particularly Deformed wing virus (DWV). Vector transmission of DWV has resulted in the accumulation of high viral loads in honeybees and is often associated with colony death. DWV has two main genotypes, A and B. DWV-A was more prevalent during the initial phase of V. destructor establishment. In recent years, the global prevalence of DWV-B has increased, suggesting that DWV-B is better adapted to vector transmission than DWV-A. We aimed to determine the role vector transmission plays in DWV genotype prevalence at a colony level. We experimentally increased or decreased the number of V. destructor mites in honeybee colonies, and tracked DWV-A and DWV-B loads over a period of 10 months. Our results show that the two DWV genotypes differ in their response to mite numbers. DWV-A accumulation in honeybees was positively correlated with mite numbers yet DWV-A was largely undetected in the absence of the mite. In contrast, colonies had high loads of DWV-B even when mite numbers were low. DWV-B loads persisted in miticide-treated colonies, indicating that this genotype has a competitive advantage over DWV-A irrespective of mite numbers. Our findings suggest that the global increase in DWV-B prevalence is not driven by selective pressure by the vector. Rather, DWV-B is able to persist in colonies at higher viral loads relative to DWV-A in the presence and absence of V. destructor. The interplay between V. destructor and DWV genotypes within honeybee colonies may have broad consequences upon viral diversity in sympatric taxa as a result of spillover.
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Affiliation(s)
- Amanda M Norton
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Emily J Remnant
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Jolanda Tom
- Wageningen University and Research, Wageningen, The Netherlands
| | - Gabriele Buchmann
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | | | - Madeleine Beekman
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Wissenschaftskolleg zu Berlin, Berlin, Germany
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Abstract
The evolutionary significance of epigenetic inheritance is controversial. While epigenetic marks such as DNA methylation can affect gene function and change in response to environmental conditions, their role as carriers of heritable information is often considered anecdotal. Indeed, near-complete DNA methylation reprogramming, as occurs during mammalian embryogenesis, is a major hindrance for the transmission of nongenetic information between generations. Yet it remains unclear how general DNA methylation reprogramming is across the tree of life. Here we investigate the existence of epigenetic inheritance in the honey bee. We studied whether fathers can transfer epigenetic information to their daughters through DNA methylation. We performed instrumental inseminations of queens, each with four different males, retaining half of each male's semen for whole genome bisulfite sequencing. We then compared the methylation profile of each father's somatic tissue and semen with the methylation profile of his daughters. We found that DNA methylation patterns were highly conserved between tissues and generations. There was a much greater similarity of methylomes within patrilines (i.e., father-daughter subfamilies) than between patrilines in each colony. Indeed, the samples' methylomes consistently clustered by patriline within colony. Samples from the same patriline had twice as many shared methylated sites and four times fewer differentially methylated regions compared to samples from different patrilines. Our findings indicate that there is no DNA methylation reprogramming in bees and, consequently, that DNA methylation marks are stably transferred between generations. This points to a greater evolutionary potential of the epigenome in invertebrates than there is in mammals.
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Affiliation(s)
- Boris Yagound
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia;
| | - Emily J Remnant
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Gabriele Buchmann
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin P Oldroyd
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
- Wissenschaftskolleg zu Berlin, 14193 Berlin, Germany
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Smith NMA, Yagound B, Remnant EJ, Foster CSP, Buchmann G, Allsopp MH, Kent CF, Zayed A, Rose SA, Lo K, Ashe A, Harpur BA, Beekman M, Oldroyd BP. Paternally-biased gene expression follows kin-selected predictions in female honey bee embryos. Mol Ecol 2020; 29:1523-1533. [PMID: 32220095 DOI: 10.1111/mec.15419] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/01/2020] [Accepted: 03/12/2020] [Indexed: 11/30/2022]
Abstract
The Kinship Theory of Genomic Imprinting (KTGI) posits that, in species where females mate with multiple males, there is selection for a male to enhance the reproductive success of his offspring at the expense of other males and his mating partner. Reciprocal crosses between honey bee subspecies show parent-of-origin effects for reproductive traits, suggesting that males modify the expression of genes related to female function in their female offspring. This effect is likely to be greater in the Cape honey bee (Apis mellifera capensis), because a male's daughters have the unique ability to produce female offspring that can develop into reproductive workers or the next queen without mating. We generated reciprocal crosses between Capensis and another subspecies and used RNA-seq to identify transcripts that are over- or underexpressed in the embryos, depending on the parental origin of the gene. As predicted, 21 genes showed expression bias towards the Capensis father's allele in colonies with a Capensis father, with no such bias in the reciprocal cross. A further six genes showed a consistent bias towards expression of the father's allele across all eight colonies examined, regardless of the direction of the cross. Consistent with predictions of the KTGI, six of the 21 genes are associated with female reproduction. No gene consistently showed overexpression of the maternal allele.
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Affiliation(s)
- Nicholas M A Smith
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Charles S P Foster
- Evolutionary and Integrative Zoology Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Michael H Allsopp
- Honey Bee Research Section, ARC-Plant Protection Research Institute, Stellenbosch, South Africa
| | - Clement F Kent
- Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Amro Zayed
- Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Stephen A Rose
- Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Kitty Lo
- Statistics Research Group, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Alyson Ashe
- Molecular Biosciences, The University of Sydney, Sydney, NSW, Australia
| | - Brock A Harpur
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
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Norton AM, Remnant EJ, Buchmann G, Beekman M. Accumulation and Competition Amongst Deformed Wing Virus Genotypes in Naïve Australian Honeybees Provides Insight Into the Increasing Global Prevalence of Genotype B. Front Microbiol 2020; 11:620. [PMID: 32328051 PMCID: PMC7160646 DOI: 10.3389/fmicb.2020.00620] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 01/24/2020] [Accepted: 03/19/2020] [Indexed: 12/27/2022] Open
Abstract
Honeybee colony deaths are often attributed to the ectoparasitic mite Varroa destructor and deformed wing virus (DWV), vectored by the mite. In the presence of V. destructor both main genotypes (DWV-A and DWV-B) have been correlated with colony loss. Studies show that DWV-B is the most prevalent genotype in the United Kingdom and Europe. More recently DWV-B has increased in prevalence in the United States. The increasing prevalence of DWV-B at the expense of DWV-A suggests that competition exists between the genotypes. Competition may be due to disparities in virulence between genotypes, differences in fitness, such as rate of replication, or a combination of factors. In this study we investigated if DWV genotypes differ in their rate of accumulation in Australian honeybees naïve to both V. destructor and DWV, and if viral load was associated with mortality in honeybee pupae. We singly and co-infected pupae with DWV-A, DWV-B, and a recombinant strain isolated from a V. destructor tolerant bee population. We monitored viral accumulation throughout pupation, up to 192 h post-injection. We found significant differences in accumulation, where DWV-A accumulated to significantly lower loads than DWV-B and the DWV-recombinant. We also found evidence of competition, where DWV-B loads were significantly reduced in the presence of DWV-A, but still accumulated to the highest loads overall. In contrast to previous studies, we found significant differences in virulence between pupae injected with DWV-A and DWV-B. The average mortality associated with DWV-B (0.4% ± 0.33 SE) and DWV-recombinant (2.2% ± 0.83 SE) injection were significantly less than observed for DWV-A (11% ± 1.2 SE). Our results suggest that a higher proportion of DWV-B infected pupae will emerge into adults, compared to DWV-A. Overall, our data suggest that low mortality in pupae and the ability of DWV-B to accumulate to higher loads relative to DWV-A even during co-infection may favor vector transmission by V. destructor, and may thus be contributing factors to the increasing prevalence of DWV-B globally.
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Affiliation(s)
- Amanda M. Norton
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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Remnant EJ, Mather N, Gillard TL, Yagound B, Beekman M. Direct transmission by injection affects competition among RNA viruses in honeybees. Proc Biol Sci 2020; 286:20182452. [PMID: 30963951 DOI: 10.1098/rspb.2018.2452] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The arrival of the ectoparasitic mite Varroa destructor on the western honeybee Apis mellifera saw a change in the diversity and prevalence of honeybee RNA viruses. One virus in particular, deformed wing virus (DWV) has become closely associated with V. destructor, leading many to conclude that V. destructor has affected viral virulence by changing the mode of transmission. While DWV is normally transmitted via feeding and faeces, V. destructor transmits viruses by direct injection. This change could have resulted in higher viral prevalence causing increased damage to the bees. Here we test the effect of a change in the mode of transmission on the composition and levels of honeybee RNA viruses in the absence of V. destructor. We find a rapid increase in levels of two viruses, sacbrood virus (SBV) and black queen cell virus (BQCV) after direct injection of viral extracts into honeybee pupae. In pupae injected with high levels of DWV extracted from symptomatic adult bees, DWV levels rapidly decline in the presence of SBV and BQCV. Further, we observe high mortality in honeybee pupae when injected with SBV and BQCV, whereas injecting pupae with high levels of DWV results in near 100% survival. Our results suggest a different explanation for the observed association between V. destructor and DWV. Instead of V. destructor causing an increase in DWV virulence, we hypothesize that direct virus inoculation, such as that mediated by a vector, quickly eliminates the most virulent honeybee viruses resulting in an association with less virulent viruses such as DWV.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Niklas Mather
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Thomas L Gillard
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
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Yagound B, Smith NMA, Buchmann G, Oldroyd BP, Remnant EJ. Unique DNA Methylation Profiles Are Associated with cis-Variation in Honey Bees. Genome Biol Evol 2019; 11:2517-2530. [PMID: 31406991 PMCID: PMC6740151 DOI: 10.1093/gbe/evz177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is an important epigenetic modification that mediates diverse processes such as cellular differentiation, phenotypic plasticity, and genomic imprinting. Mounting evidence suggests that local DNA sequence variation can be associated with particular DNA methylation states, indicating that the interplay between genetic and epigenetic factors may contribute synergistically to the phenotypic complexity of organisms. Social insects such as ants, bees, and wasps have extensive phenotypic plasticity manifested in their different castes, and this plasticity has been associated with variation in DNA methylation. Yet, the influence of genetic variation on DNA methylation state remains mostly unknown. Here we examine the importance of sequence-specific methylation at the genome-wide level, using whole-genome bisulfite sequencing of the semen of individual honey bee males. We find that individual males harbor unique DNA methylation patterns in their semen, and that genes that are more variable at the epigenetic level are also more likely to be variable at the genetic level. DNA sequence variation can affect DNA methylation by modifying CG sites directly, but can also be associated with local variation in cis that is not CG-site specific. We show that covariation in sequence polymorphism and DNA methylation state contributes to the individual-specificity of epigenetic marks in social insects, which likely promotes their retention across generations, and their capacity to influence evolutionary adaptation.
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Affiliation(s)
- Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Nicholas M A Smith
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
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Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. J Virol 2017; 91:e00158-17. [PMID: 28515299 PMCID: PMC5533899 DOI: 10.1128/jvi.00158-17] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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Remnant EJ, Ashe A, Young PE, Buchmann G, Beekman M, Allsopp MH, Suter CM, Drewell RA, Oldroyd BP. Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation. BMC Genomics 2016; 17:226. [PMID: 26969617 PMCID: PMC4788913 DOI: 10.1186/s12864-016-2506-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 10/27/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes. RESULTS We compared genome-wide methylation patterns of sexually-produced, diploid embryos laid by a queen, with parthenogenetically-produced diploid embryos laid by her daughters. Thelytokous embryos inheriting two maternal genomes had fewer hypermethylated genes compared to fertilized embryos, supporting the prediction that fertilized embryos have increased methylation due to inheritance of a paternal genome. However, bisulfite PCR and sequencing of a differentially methylated gene, Stan (GB18207) showed strong allele-specific methylation that was maintained in both fertilized and thelytokous embryos. For this gene, methylation was associated with haplotype, not parent of origin. CONCLUSIONS The results of our study are consistent with predictions from the kin theory of genomic imprinting. However, our demonstration of allele-specific methylation based on sequence shows that genome-wide differential methylation studies can potentially confound imprinting and allele-specific methylation. It further suggests that methylation patterns are heritable or that specific sequence motifs are targets for methylation in some genes.
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Affiliation(s)
- Emily J. Remnant
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Alyson Ashe
- />School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006 Australia
| | - Paul E. Young
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Gabriele Buchmann
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Madeleine Beekman
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Michael H. Allsopp
- />Honey Bee Research Section, ARC-Plant Protection Research Institute, Private Bag X5017, Stellenbosch, South Africa
| | - Catherine M. Suter
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Robert A. Drewell
- />Biology Department, Clark University, 950 Main Street, Worcester, MA 01610 USA
| | - Benjamin P. Oldroyd
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
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Remnant EJ, Morton CJ, Daborn PJ, Lumb C, Yang YT, Ng HL, Parker MW, Batterham P. The role of Rdl in resistance to phenylpyrazoles in Drosophila melanogaster. Insect Biochem Mol Biol 2014; 54:11-21. [PMID: 25193377 DOI: 10.1016/j.ibmb.2014.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 06/03/2023]
Abstract
Extensive use of older generation insecticides may result in pre-existing cross-resistance to new chemical classes acting at the same target site. Phenylpyrazole insecticides block inhibitory neurotransmission in insects via their action on ligand-gated chloride channels (LGCCs). Phenylpyrazoles are broad-spectrum insecticides widely used in agriculture and domestic pest control. So far, all identified cases of target site resistance to phenylpyrazoles are based on mutations in the Rdl (Resistance to dieldrin) LGCC subunit, the major target site for cyclodiene insecticides. We examined the role that mutations in Rdl have on phenylpyrazole resistance in Drosophila melanogaster, exploring naturally occurring variation, and generating predicted resistance mutations by mutagenesis. Natural variation at the Rdl locus in inbred strains of D. melanogaster included gene duplication, and a line containing two Rdl mutations found in a highly resistant line of Drosophila simulans. These mutations had a moderate impact on survival following exposure to two phenylpyrazoles, fipronil and pyriprole. Homology modelling suggested that the Rdl chloride channel pore contains key residues for binding fipronil and pyriprole. Mutagenesis of these sites and assessment of resistance in vivo in transgenic lines showed that amino acid identity at the Ala(301) site influenced resistance levels, with glycine showing greater survival than serine replacement. We confirm that point mutations at the Rdl 301 site provide moderate resistance to phenylpyrazoles in D. melanogaster. We also emphasize the beneficial aspects of testing predicted mutations in a whole organism to validate a candidate gene approach.
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Affiliation(s)
- Emily J Remnant
- Department of Genetics and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia; School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Craig J Morton
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, VIC 3056, Australia
| | - Phillip J Daborn
- Department of Genetics and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Christopher Lumb
- Department of Genetics and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Ying Ting Yang
- Department of Genetics and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Hooi Ling Ng
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, VIC 3056, Australia
| | - Michael W Parker
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, VIC 3056, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Philip Batterham
- Department of Genetics and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3052, Australia
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Drewell RA, Bush EC, Remnant EJ, Wong GT, Beeler SM, Stringham JL, Lim J, Oldroyd BP. The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera. Development 2014; 141:2702-11. [PMID: 24924193 PMCID: PMC4067964 DOI: 10.1242/dev.110163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [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: 01/03/2023]
Abstract
In honey bees (Apis mellifera), the epigenetic mark of DNA methylation is central to the developmental regulation of caste differentiation, but may also be involved in additional biological functions. In this study, we examine the whole genome methylation profiles of three stages of the haploid honey bee genome: unfertilised eggs, the adult drones that develop from these eggs and the sperm produced by these drones. These methylomes reveal distinct patterns of methylation. Eggs and sperm show 381 genes with significantly different CpG methylation patterns, with the vast majority being more methylated in eggs. Adult drones show greatly reduced levels of methylation across the genome when compared with both gamete samples. This suggests a dynamic cycle of methylation loss and gain through the development of the drone and during spermatogenesis. Although fluxes in methylation during embryogenesis may account for some of the differentially methylated sites, the distinct methylation patterns at some genes suggest parent-specific epigenetic marking in the gametes. Extensive germ line methylation of some genes possibly explains the lower-than-expected frequency of CpG sites in these genes. We discuss the potential developmental and evolutionary implications of methylation in eggs and sperm in this eusocial insect species.
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Affiliation(s)
- Robert A Drewell
- Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Eliot C Bush
- Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA
| | - Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Biological Sciences A12, University of Sydney, Sydney, NSW 2006, Australia
| | - Garrett T Wong
- Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA
| | - Suzannah M Beeler
- Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA
| | - Jessica L Stringham
- Computer Science Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA
| | - Julianne Lim
- Behaviour and Genetics of Social Insects Laboratory, School of Biological Sciences A12, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, School of Biological Sciences A12, University of Sydney, Sydney, NSW 2006, Australia
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Remnant EJ, Koetz A, Tan K, Hinson E, Beekman M, Oldroyd BP. Reproductive interference between honeybee species in artificial sympatry. Mol Ecol 2014; 23:1096-107. [DOI: 10.1111/mec.12669] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/05/2014] [Accepted: 01/10/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Emily J. Remnant
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
| | - Anna Koetz
- Biosecurity Queensland; Department of Agriculture; Fisheries and Forestry; PO Box 652 Cairns QLD 4870 Australia
| | - Ken Tan
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Science; Kunming Yunnan Province 650223 China
| | - Eloise Hinson
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
| | - Benjamin P. Oldroyd
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
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Abstract
Apis mellifera capensis is unique among honeybees in that unmated workers can produce pseudo-clonal female offspring via thelytokous parthenogenesis. Workers use this ability to compete among themselves and with their queen to be the mother of new queens. Males could therefore enhance their reproductive success by imprinting genes that enhance fertility in their daughter workers. This possibility sets the scene for intragenomic conflict between queens and drones over worker reproductive traits. Here, we show a strong parent-of-origin effect for ovary size (number of ovarioles) in reciprocal crosses between two honeybee subspecies, A. m. capensis and Apis mellifera scutellata. In this cross, workers with an A. m. capensis father had 30% more ovarioles than genotypically matched workers with an A. m. scutellata father. Other traits we measured (worker weight at emergence and the presence/absence of a spermatheca) are influenced more by rearing conditions than by parent-of-origin effects. Our study is the first to show a strong epigenetic (or, less likely, cytoplasmic maternal) effect for a reproductive trait in the honeybee and suggests that a search for parent-of-origin effects in other social insects may be fruitful.
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Affiliation(s)
- Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, School of Biological Sciences, University of Sydney, , Sydney, New South Wales 2006, Australia, Honey Bee Research Section, ARC-Plant Protection Research Institute, , Private Bag X5017, Stellenbosch 7599, South Africa, Department of Biology, Harvey Mudd College, , 301 Platt Boulevard, Claremont, CA 91001, USA
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Remnant EJ, Good RT, Schmidt JM, Lumb C, Robin C, Daborn PJ, Batterham P. Gene duplication in the major insecticide target site, Rdl, in Drosophila melanogaster. Proc Natl Acad Sci U S A 2013; 110:14705-10. [PMID: 23959864 PMCID: PMC3767507 DOI: 10.1073/pnas.1311341110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Resistance to Dieldrin gene, Rdl, encodes a GABA-gated chloride channel subunit that is targeted by cyclodiene and phenylpyrazole insecticides. The gene was first characterized in Drosophila melanogaster by genetic mapping of resistance to the cyclodiene dieldrin. The 4,000-fold resistance observed was due to a single amino acid replacement, Ala(301) to Ser. The equivalent change was subsequently identified in Rdl orthologs of a large range of resistant insect species. Here, we report identification of a duplication at the Rdl locus in D. melanogaster. The 113-kb duplication contains one WT copy of Rdl and a second copy with two point mutations: an Ala(301) to Ser resistance mutation and Met(360) to Ile replacement. Individuals with this duplication exhibit intermediate dieldrin resistance compared with single copy Ser(301) homozygotes, reduced temperature sensitivity, and altered RNA editing associated with the resistant allele. Ectopic recombination between Roo transposable elements is involved in generating this genomic rearrangement. The duplication phenotypes were confirmed by construction of a transgenic, artificial duplication integrating the 55.7-kb Rdl locus with a Ser(301) change into an Ala(301) background. Gene duplications can contribute significantly to the evolution of insecticide resistance, most commonly by increasing the amount of gene product produced. Here however, duplication of the Rdl target site creates permanent heterozygosity, providing unique potential for adaptive mutations to accrue in one copy, without abolishing the endogenous role of an essential gene.
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Affiliation(s)
- Emily J Remnant
- Department of Genetics and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia.
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