New Results
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
1Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA.
2Howard Hughes Medical Institute, New York, New York, USA.
3Kavli Neural Systems Institute, New York, New York, USA.
Olga Dudchenko
4The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
5Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
6Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
7Center for Theoretical and Biological Physics, Rice University, Houston, Texas, USA.
Sarah Kingan
8Pacific Biosciences, Menlo Park, California, USA.
Sergey Koren
9National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
Igor Antoshechkin
10Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.
Jacob E. Crawford
11Verily Life Sciences, South San Francisco, California, USA.
William J. Glassford
12Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
Margaret Herre
1Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA.
3Kavli Neural Systems Institute, New York, New York, USA.
Seth N. Redmond
13Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
14Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Noah H. Rose
15Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.
Gareth D. Weedall
16Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
17Liverpool John Moores University, Liverpool, United Kingdom.
Yang Wu
18Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China.
19Department of Biochemistry, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Sanjit S. Batra
4The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
5Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
6Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
Carlos A. Brito-Sierra
20Department of Entomology, Purdue University, West Lafayette, Indiana, USA.
21Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
Steven D. Buckingham
22Centre for Respiratory Biology, UCL Respiratory, University College London, London, United Kingdom.
Corey L Campbell
23Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Saki Chan
24Bionano Genomics, San Diego, California, USA.
Eric Cox
25National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Benjamin R. Evans
26Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Thanyalak Fansiri
27Vector Biology and Control Section, Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand.
Igor Filipović
28Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Albin Fontaine
29Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
30Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.
31Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France.
32Aix Marseille Université, IRD (Dakar, Marseille, Papeete), AP-HM, IHU - Méditerranée Infection, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.
Andrea Gloria-Soria
26Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Richard Hall
8Pacific Biosciences, Menlo Park, California, USA.
Vinita S. Joardar
25National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Andrew K. Jones
33Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.
Raissa G.G. Kay
34Department of Entomology, University of California Riverside, Riverside, California, USA.
Vamsi K. Kodali
25National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Joyce Lee
24Bionano Genomics, San Diego, California, USA.
Gareth J. Lycett
16Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
Sara N. Mitchell
11Verily Life Sciences, South San Francisco, California, USA.
Jill Muehling
8Pacific Biosciences, Menlo Park, California, USA.
Michael R. Murphy
25National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Arina D. Omer
4The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
5Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
6Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
Frederick A. Partridge
22Centre for Respiratory Biology, UCL Respiratory, University College London, London, United Kingdom.
Paul Peluso
8Pacific Biosciences, Menlo Park, California, USA.
Aviva Presser Aiden
4The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
5Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
35Department of Bioengineering, Rice University, Houston, Texas, USA.
36Department of Pediatrics, Texas Children’s Hospital, Houston, Texas, USA.
Vidya Ramasamy
33Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.
Gordana Rašić
28Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Sourav Roy
37Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, California, USA.
Karla Saavedra-Rodriguez
23Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Shruti Sharan
20Department of Entomology, Purdue University, West Lafayette, Indiana, USA.
21Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
Atashi Sharma
38Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Melissa Laird Smith
8Pacific Biosciences, Menlo Park, California, USA.
Joe Turner
39Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
Allison M. Weakley
11Verily Life Sciences, South San Francisco, California, USA.
Zhilei Zhao
15Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.
Omar S. Akbari
40Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA.
William C. Black IV
23Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Han Cao
24Bionano Genomics, San Diego, California, USA.
Alistair C. Darby
39Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
Catherine Hill
20Department of Entomology, Purdue University, West Lafayette, Indiana, USA.
21Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
J. Spencer Johnston
41Department of Entomology, Texas A&M University, College Station, Texas, USA.
Terence D. Murphy
25National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Alexander S. Raikhel
37Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, California, USA.
David B. Sattelle
22Centre for Respiratory Biology, UCL Respiratory, University College London, London, United Kingdom.
Igor V. Sharakhov
38Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
42Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia.
Bradley J. White
11Verily Life Sciences, South San Francisco, California, USA.
Li Zhao
43Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, New York, USA.
Erez Lieberman Aiden
4The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, USA.
5Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
6Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, USA.
7Center for Theoretical and Biological Physics, Rice University, Houston, Texas, USA.
13Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Richard S. Mann
12Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
Louis Lambrechts
29Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
31Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France.
Jeffrey R. Powell
26Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Maria V. Sharakhova
38Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
42Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia.
Zhijian Tu
19Department of Biochemistry, Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, USA.
Hugh M. Robertson
44Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Carolyn S. McBride
15Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.
45Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA.
Alex R. Hastie
24Bionano Genomics, San Diego, California, USA.
Jonas Korlach
8Pacific Biosciences, Menlo Park, California, USA.
Daniel E. Neafsey
13Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
14Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
Adam M. Phllippy
9National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
Leslie B. Vosshall
1Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA.
2Howard Hughes Medical Institute, New York, New York, USA.
3Kavli 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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