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Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control
View ORCID ProfileBenjamin J. Matthews, View ORCID ProfileOlga Dudchenko, View ORCID ProfileSarah Kingan, View ORCID ProfileSergey Koren, View ORCID ProfileIgor Antoshechkin, View ORCID ProfileJacob E. Crawford, View ORCID ProfileWilliam J. Glassford, View ORCID ProfileMargaret Herre, View ORCID ProfileSeth N. Redmond, View ORCID ProfileNoah H. Rose, View ORCID ProfileGareth D. Weedall, View ORCID ProfileYang Wu, View ORCID ProfileSanjit S. Batra, View ORCID ProfileCarlos A. Brito-Sierra, View ORCID ProfileSteven D. Buckingham, View ORCID ProfileCorey L Campbell, View ORCID ProfileSaki Chan, View ORCID ProfileEric Cox, View ORCID ProfileBenjamin R. Evans, View ORCID ProfileThanyalak Fansiri, View ORCID ProfileIgor Filipović, View ORCID ProfileAlbin Fontaine, View ORCID ProfileAndrea Gloria-Soria, View ORCID ProfileRichard Hall, View ORCID ProfileVinita S. Joardar, View ORCID ProfileAndrew K. Jones, View ORCID ProfileRaissa G.G. Kay, View ORCID ProfileVamsi K. Kodali, View ORCID ProfileJoyce Lee, View ORCID ProfileGareth J. Lycett, View ORCID ProfileSara N. Mitchell, View ORCID ProfileJill Muehling, View ORCID ProfileMichael R. Murphy, View ORCID ProfileArina D. Omer, View ORCID ProfileFrederick A. Partridge, View ORCID ProfilePaul Peluso, View ORCID ProfileAviva Presser Aiden, View ORCID ProfileVidya Ramasamy, View ORCID ProfileGordana Rašić, View ORCID ProfileSourav Roy, View ORCID ProfileKarla Saavedra-Rodriguez, View ORCID ProfileShruti Sharan, View ORCID ProfileAtashi Sharma, View ORCID ProfileMelissa Laird Smith, View ORCID ProfileJoe Turner, View ORCID ProfileAllison M. Weakley, View ORCID ProfileZhilei Zhao, View ORCID ProfileOmar S. Akbari, View ORCID ProfileWilliam C. Black IV, View ORCID ProfileHan Cao, View ORCID ProfileAlistair C. Darby, View ORCID ProfileCatherine Hill, View ORCID ProfileJ. Spencer Johnston, View ORCID ProfileTerence D. Murphy, View ORCID ProfileAlexander S. Raikhel, View ORCID ProfileDavid B. Sattelle, View ORCID ProfileIgor V. Sharakhov, View ORCID ProfileBradley J. White, View ORCID ProfileLi Zhao, View ORCID ProfileErez Lieberman Aiden, View ORCID ProfileRichard S. Mann, View ORCID ProfileLouis Lambrechts, View ORCID ProfileJeffrey R. Powell, View ORCID ProfileMaria V. Sharakhova, View ORCID ProfileZhijian Tu, View ORCID ProfileHugh M. Robertson, View ORCID ProfileCarolyn S. McBride, View ORCID ProfileAlex R. Hastie, View ORCID ProfileJonas Korlach, View ORCID ProfileDaniel E. Neafsey, View ORCID ProfileAdam M. Phllippy, View ORCID ProfileLeslie B. Vosshall
doi: https://doi.org/10.1101/240747
Benjamin J. Matthews
Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA.
Howard Hughes Medical Institute, New York, New York, USA.
Kavli Neural Systems Institute, New York, New York, USA.
Olga Dudchenko
The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
Center for Theoretical and Biological Physics, Rice University, Houston, Texas, USA.
Sarah Kingan
Pacific Biosciences, Menlo Park, California, USA.
Sergey Koren
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
Igor Antoshechkin
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.
Jacob E. Crawford
Verily Life Sciences, South San Francisco, California, USA.
William J. Glassford
Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
Margaret Herre
Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA.
Kavli Neural Systems Institute, New York, New York, USA.
Seth N. Redmond
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Noah H. Rose
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.
Gareth D. Weedall
Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
Liverpool John Moores University, Liverpool, United Kingdom.
Yang Wu
Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China.
Department of Biochemistry, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Sanjit S. Batra
The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
Carlos A. Brito-Sierra
Department of Entomology, Purdue University, West Lafayette, Indiana, USA.
Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
Steven D. Buckingham
Centre for Respiratory Biology, UCL Respiratory, University College London, London, United Kingdom.
Corey L Campbell
Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Saki Chan
Bionano Genomics, San Diego, California, USA.
Eric Cox
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Benjamin R. Evans
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Thanyalak Fansiri
Vector Biology and Control Section, Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand.
Igor Filipović
Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Albin Fontaine
Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.
Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France.
Aix Marseille Université, IRD (Dakar, Marseille, Papeete), AP-HM, IHU - Méditerranée Infection, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.
Andrea Gloria-Soria
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Richard Hall
Pacific Biosciences, Menlo Park, California, USA.
Vinita S. Joardar
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Andrew K. Jones
Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.
Raissa G.G. Kay
Department of Entomology, University of California Riverside, Riverside, California, USA.
Vamsi K. Kodali
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Joyce Lee
Bionano Genomics, San Diego, California, USA.
Gareth J. Lycett
Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
Sara N. Mitchell
Verily Life Sciences, South San Francisco, California, USA.
Jill Muehling
Pacific Biosciences, Menlo Park, California, USA.
Michael R. Murphy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Arina D. Omer
The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
Frederick A. Partridge
Centre for Respiratory Biology, UCL Respiratory, University College London, London, United Kingdom.
Paul Peluso
Pacific Biosciences, Menlo Park, California, USA.
Aviva Presser Aiden
The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Department of Bioengineering, Rice University, Houston, Texas, USA.
Department of Pediatrics, Texas Children’s Hospital, Houston, Texas, USA.
Vidya Ramasamy
Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.
Gordana Rašić
Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Sourav Roy
Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, California, USA.
Karla Saavedra-Rodriguez
Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Shruti Sharan
Department of Entomology, Purdue University, West Lafayette, Indiana, USA.
Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
Atashi Sharma
Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Melissa Laird Smith
Pacific Biosciences, Menlo Park, California, USA.
Joe Turner
Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
Allison M. Weakley
Verily Life Sciences, South San Francisco, California, USA.
Zhilei Zhao
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.
Omar S. Akbari
Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA.
William C. Black
Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Han Cao
Bionano Genomics, San Diego, California, USA.
Alistair C. Darby
Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
Catherine Hill
Department of Entomology, Purdue University, West Lafayette, Indiana, USA.
Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
J. Spencer Johnston
Department of Entomology, Texas A&M University, College Station, Texas, USA.
Terence D. Murphy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Alexander S. Raikhel
Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, California, USA.
David B. Sattelle
Centre for Respiratory Biology, UCL Respiratory, University College London, London, United Kingdom.
Igor V. Sharakhov
Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia.
Bradley J. White
Verily Life Sciences, South San Francisco, California, USA.
Li Zhao
Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, New York, USA.
Erez Lieberman Aiden
The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
Center for Theoretical and Biological Physics, Rice University, Houston, Texas, USA.
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Richard S. Mann
Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
Louis Lambrechts
Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France.
Jeffrey R. Powell
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Maria V. Sharakhova
Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia.
Zhijian Tu
Department of Biochemistry, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Hugh M. Robertson
Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Carolyn S. McBride
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.
Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Alex R. Hastie
Bionano Genomics, San Diego, California, USA.
Jonas Korlach
Pacific Biosciences, Menlo Park, California, USA.
Daniel E. Neafsey
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Adam M. Phllippy
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
Leslie B. Vosshall
Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA.
Howard Hughes Medical Institute, New York, New York, USA.
Kavli Neural Systems Institute, New York, New York, USA.
Abstract
Female Aedes aegypti mosquitoes infect hundreds of millions of people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding the biology of this insect, and developing tools to fight it, has been slowed by the lack of a high-quality genome assembly. Here we combine diverse genome technologies to produce AaegL5, a dramatically improved and annotated assembly, and demonstrate how it accelerates mosquito science and control. We anchored the physical and cytogenetic maps, resolved the size and composition of the elusive sex-determining “M locus”, significantly increased the known members of the glutathione-S-transferase genes important for insecticide resistance, and doubled the number of chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites. Using high-resolution QTL and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. We predict that AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly arboviral vector.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Posted December 29, 2017.
Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control
Benjamin J. Matthews, Olga Dudchenko, Sarah Kingan, Sergey Koren, Igor Antoshechkin, Jacob E. Crawford, William J. Glassford, Margaret Herre, Seth N. Redmond, Noah H. Rose, Gareth D. Weedall, Yang Wu, Sanjit S. Batra, Carlos A. Brito-Sierra, Steven D. Buckingham, Corey L Campbell, Saki Chan, Eric Cox, Benjamin R. Evans, Thanyalak Fansiri, Igor Filipović, Albin Fontaine, Andrea Gloria-Soria, Richard Hall, Vinita S. Joardar, Andrew K. Jones, Raissa G.G. Kay, Vamsi K. Kodali, Joyce Lee, Gareth J. Lycett, Sara N. Mitchell, Jill Muehling, Michael R. Murphy, Arina D. Omer, Frederick A. Partridge, Paul Peluso, Aviva Presser Aiden, Vidya Ramasamy, Gordana Rašić, Sourav Roy, Karla Saavedra-Rodriguez, Shruti Sharan, Atashi Sharma, Melissa Laird Smith, Joe Turner, Allison M. Weakley, Zhilei Zhao, Omar S. Akbari, William C. Black IV, Han Cao, Alistair C. Darby, Catherine Hill, J. Spencer Johnston, Terence D. Murphy, Alexander S. Raikhel, David B. Sattelle, Igor V. Sharakhov, Bradley J. White, Li Zhao, Erez Lieberman Aiden, Richard S. Mann, Louis Lambrechts, Jeffrey R. Powell, Maria V. Sharakhova, Zhijian Tu, Hugh M. Robertson, Carolyn S. McBride, Alex R. Hastie, Jonas Korlach, Daniel E. Neafsey, Adam M. Phllippy, Leslie B. Vosshall
bioRxiv 240747; doi: https://doi.org/10.1101/240747
Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control
Benjamin J. Matthews, Olga Dudchenko, Sarah Kingan, Sergey Koren, Igor Antoshechkin, Jacob E. Crawford, William J. Glassford, Margaret Herre, Seth N. Redmond, Noah H. Rose, Gareth D. Weedall, Yang Wu, Sanjit S. Batra, Carlos A. Brito-Sierra, Steven D. Buckingham, Corey L Campbell, Saki Chan, Eric Cox, Benjamin R. Evans, Thanyalak Fansiri, Igor Filipović, Albin Fontaine, Andrea Gloria-Soria, Richard Hall, Vinita S. Joardar, Andrew K. Jones, Raissa G.G. Kay, Vamsi K. Kodali, Joyce Lee, Gareth J. Lycett, Sara N. Mitchell, Jill Muehling, Michael R. Murphy, Arina D. Omer, Frederick A. Partridge, Paul Peluso, Aviva Presser Aiden, Vidya Ramasamy, Gordana Rašić, Sourav Roy, Karla Saavedra-Rodriguez, Shruti Sharan, Atashi Sharma, Melissa Laird Smith, Joe Turner, Allison M. Weakley, Zhilei Zhao, Omar S. Akbari, William C. Black IV, Han Cao, Alistair C. Darby, Catherine Hill, J. Spencer Johnston, Terence D. Murphy, Alexander S. Raikhel, David B. Sattelle, Igor V. Sharakhov, Bradley J. White, Li Zhao, Erez Lieberman Aiden, Richard S. Mann, Louis Lambrechts, Jeffrey R. Powell, Maria V. Sharakhova, Zhijian Tu, Hugh M. Robertson, Carolyn S. McBride, Alex R. Hastie, Jonas Korlach, Daniel E. Neafsey, Adam M. Phllippy, Leslie B. Vosshall
bioRxiv 240747; doi: https://doi.org/10.1101/240747
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